Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is
moderately expressed , only 33.3% of the average gene in this release. The
sequence of this gene is defined by
41 GenBank accessions from 38 cDNA clones, some from testis (seen 24 times), blood (2), natural killer cells, cell line (2), brain (once), lung tumor (once), medulla (once). We annotate
structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains
31 distinct gt-ag introns . Transcription produces
9 alternatively spliced mRNAs . There are 5 probable
alternative promotors , 4 non overlapping alternative last exons and 3 validated
alternative polyadenylation sites (see the
diagram ). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 4
cassette exons , overlapping exons with different boundaries, splicing versus retention of one intron. 676 bp of this gene
are antisense to spliced gene DHX38 , raising the possibility of regulated alternate expression.
Note that mRNA .dAug10 was found
in vivo , although it is a predicted target of
nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (
uORF ) initiating at an AUG upstream of the main open reading frame (in variant aAug10, bAug10).
Function: There are
2 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a
disease (Infertility, Male). Proteins are expected to
localize in various compartments (nucleus, cytoplasm).
Protein coding potential: 8 spliced mRNAs putatively encode
good proteins , altogether
8 different isoforms (4 complete, 2 COOH complete, 2 partial ), some containing a second peroximal domain, a coiled coil stretch
[Psort2] . The remaining mRNA variant (spliced; partial) appears not to encode a good protein. Finally proteins from this gene may be modulated by
acetylation; di-methylation; mono-methylation; phosphorylation , as detailed at PhosphoSite.
Please quote:
AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
Gene PMFBP1
5'
3'
encoded on minus strand of chromosome 16 from 72,210,777 to 72,146,069
16
261
686
305
330
680
780
663
589
65
684
799
677
1020
1995
1905
1764
1725
1374
a
16
261
686
305
330
680
780
663
589
660
684
799
677
1020
1995
1905
1764
1725
1374
b
[NM]
6
261
48
57
305
330
680
780
663
589
660
684
799
677
1020
1995
1905
1764
1725
231
c
[NM]
54
145
261
i
330
680
780
663
589
660
684
799
677
49
13
1995
1905
d
6
261
686
e
1764
1725
33
f
1
261
686
g
16
261
48
57
h
5kb
0
201 bp exon
201 bp exon
21 bp uORF
201 bp exon
785 bp [gt-ag] intron
16 GenBank accessions
72 bp exon
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
153 bp exon
10304 bp [gt-ag] intron
19 GenBank accessions
667 RNA-seq supporting reads
117 UHR pooled cells
56 Brain
132 Blood
346 Neuroblastoma
16 Other
(also 262 Primates bodymap)
249 bp exon
249 bp exon
3381 bp [gt-ag] intron
10 GenBank accessions
295 RNA-seq supporting reads
84 UHR pooled cells
14 Brain
40 Blood
145 Neuroblastoma
12 Other
(also 218 Primates bodymap)
222 bp exon
222 bp exon
10025 bp [gt-ag] intron
10 GenBank accessions
320 RNA-seq supporting reads
105 UHR pooled cells
29 Brain
62 Blood
122 Neuroblastoma
2 Other
(also 107 Primates bodymap)
171 bp exon
171 bp exon
1012 bp [gt-ag] intron
10 GenBank accessions
670 RNA-seq supporting reads
152 UHR pooled cells
49 Brain
83 Blood
371 Neuroblastoma
15 Other
(also 160 Primates bodymap)
111 bp exon
111 bp exon
2469 bp [gt-ag] intron
11 GenBank accessions
769 RNA-seq supporting reads
181 UHR pooled cells
43 Brain
101 Blood
423 Neuroblastoma
21 Other
(also 186 Primates bodymap)
127 bp exon
127 bp exon
87 bp [gt-ag] intron
11 GenBank accessions
652 RNA-seq supporting reads
114 UHR pooled cells
61 Brain
96 Blood
356 Neuroblastoma
25 Other
(also 192 Primates bodymap)
158 bp exon
158 bp exon
3456 bp [gt-ag] intron
10 GenBank accessions
579 RNA-seq supporting reads
123 UHR pooled cells
38 Brain
92 Blood
307 Neuroblastoma
19 Other
(also 154 Primates bodymap)
259 bp exon
259 bp exon
2010 bp [gt-ag] intron
1 GenBank accession
64 RNA-seq supporting reads
6 UHR pooled cells
10 Blood
48 Neuroblastoma
(also 8 Primates bodymap)
190 bp exon
190 bp exon
175 bp [gt-ag] intron
8 GenBank accessions
676 RNA-seq supporting reads
167 UHR pooled cells
50 Brain
88 Blood
348 Neuroblastoma
23 Other
(also 144 Primates bodymap)
145 bp exon
145 bp exon
979 bp [gt-ag] intron
9 GenBank accessions
790 RNA-seq supporting reads
173 UHR pooled cells
70 Brain
111 Blood
410 Neuroblastoma
26 Other
(also 62 Primates bodymap)
168 bp exon
168 bp exon
271 bp [gt-ag] intron
9 GenBank accessions
668 RNA-seq supporting reads
180 UHR pooled cells
76 Brain
42 Blood
357 Neuroblastoma
13 Other
(also 79 Primates bodymap)
138 bp exon
138 bp exon
2524 bp [gt-ag] intron
7 GenBank accessions
1013 RNA-seq supporting reads
225 UHR pooled cells
70 Brain
88 Blood
612 Neuroblastoma
18 Other
(also 155 Primates bodymap)
165 bp exon
165 bp exon
562 bp [gt-ag] intron
10 GenBank accessions
1985 RNA-seq supporting reads
425 UHR pooled cells
106 Brain
125 Blood
1310 Neuroblastoma
19 Other
(also 238 Primates bodymap)
168 bp exon
168 bp exon
303 bp [gt-ag] intron
11 GenBank accessions
1894 RNA-seq supporting reads
402 UHR pooled cells
134 Brain
125 Blood
1201 Neuroblastoma
32 Other
(also 144 Primates bodymap)
168 bp exon
168 bp exon
1117 bp [gt-ag] intron
11 GenBank accessions
1753 RNA-seq supporting reads
401 UHR pooled cells
188 Brain
95 Blood
1044 Neuroblastoma
25 Other
(also 128 Primates bodymap)
104 bp exon
104 bp exon
557 bp [gt-ag] intron
12 GenBank accessions
1713 RNA-seq supporting reads
358 UHR pooled cells
151 Brain
103 Blood
1084 Neuroblastoma
17 Other
(also 191 Primates bodymap)
75 bp exon
75 bp exon
2824 bp [gt-ag] intron
10 GenBank accessions
1364 RNA-seq supporting reads
298 UHR pooled cells
121 Brain
50 Blood
871 Neuroblastoma
24 Other
(also 212 Primates bodymap)
992 bp exon
992 bp exon
5 accessions, some from testis (seen 5 times)
capped 5' end, 4 accessions
Validated 3' end, 1 accession
992 bp exon
112 bp exon
112 bp exon
90 bp uORF
785 bp [gt-ag] intron
16 GenBank accessions
90 bp uORF
72 bp exon
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
153 bp exon
10304 bp [gt-ag] intron
19 GenBank accessions
667 RNA-seq supporting reads
117 UHR pooled cells
56 Brain
132 Blood
346 Neuroblastoma
16 Other
(also 262 Primates bodymap)
249 bp exon
249 bp exon
3381 bp [gt-ag] intron
10 GenBank accessions
295 RNA-seq supporting reads
84 UHR pooled cells
14 Brain
40 Blood
145 Neuroblastoma
12 Other
(also 218 Primates bodymap)
222 bp exon
222 bp exon
10025 bp [gt-ag] intron
10 GenBank accessions
320 RNA-seq supporting reads
105 UHR pooled cells
29 Brain
62 Blood
122 Neuroblastoma
2 Other
(also 107 Primates bodymap)
171 bp exon
171 bp exon
1012 bp [gt-ag] intron
10 GenBank accessions
670 RNA-seq supporting reads
152 UHR pooled cells
49 Brain
83 Blood
371 Neuroblastoma
15 Other
(also 160 Primates bodymap)
111 bp exon
111 bp exon
2469 bp [gt-ag] intron
11 GenBank accessions
769 RNA-seq supporting reads
181 UHR pooled cells
43 Brain
101 Blood
423 Neuroblastoma
21 Other
(also 186 Primates bodymap)
127 bp exon
127 bp exon
87 bp [gt-ag] intron
11 GenBank accessions
652 RNA-seq supporting reads
114 UHR pooled cells
61 Brain
96 Blood
356 Neuroblastoma
25 Other
(also 192 Primates bodymap)
158 bp exon
158 bp exon
3456 bp [gt-ag] intron
10 GenBank accessions
579 RNA-seq supporting reads
123 UHR pooled cells
38 Brain
92 Blood
307 Neuroblastoma
19 Other
(also 154 Primates bodymap)
244 bp exon
244 bp exon
2025 bp [gt-ag] intron
9 GenBank accessions
651 RNA-seq supporting reads
148 UHR pooled cells
56 Brain
85 Blood
336 Neuroblastoma
26 Other
(also 155 Primates bodymap)
190 bp exon
190 bp exon
175 bp [gt-ag] intron
8 GenBank accessions
676 RNA-seq supporting reads
167 UHR pooled cells
50 Brain
88 Blood
348 Neuroblastoma
23 Other
(also 144 Primates bodymap)
145 bp exon
145 bp exon
979 bp [gt-ag] intron
9 GenBank accessions
790 RNA-seq supporting reads
173 UHR pooled cells
70 Brain
111 Blood
410 Neuroblastoma
26 Other
(also 62 Primates bodymap)
168 bp exon
168 bp exon
271 bp [gt-ag] intron
9 GenBank accessions
668 RNA-seq supporting reads
180 UHR pooled cells
76 Brain
42 Blood
357 Neuroblastoma
13 Other
(also 79 Primates bodymap)
138 bp exon
138 bp exon
2524 bp [gt-ag] intron
7 GenBank accessions
1013 RNA-seq supporting reads
225 UHR pooled cells
70 Brain
88 Blood
612 Neuroblastoma
18 Other
(also 155 Primates bodymap)
165 bp exon
165 bp exon
562 bp [gt-ag] intron
10 GenBank accessions
1985 RNA-seq supporting reads
425 UHR pooled cells
106 Brain
125 Blood
1310 Neuroblastoma
19 Other
(also 238 Primates bodymap)
168 bp exon
168 bp exon
303 bp [gt-ag] intron
11 GenBank accessions
1894 RNA-seq supporting reads
402 UHR pooled cells
134 Brain
125 Blood
1201 Neuroblastoma
32 Other
(also 144 Primates bodymap)
168 bp exon
168 bp exon
1117 bp [gt-ag] intron
11 GenBank accessions
1753 RNA-seq supporting reads
401 UHR pooled cells
188 Brain
95 Blood
1044 Neuroblastoma
25 Other
(also 128 Primates bodymap)
104 bp exon
104 bp exon
557 bp [gt-ag] intron
12 GenBank accessions
1713 RNA-seq supporting reads
358 UHR pooled cells
151 Brain
103 Blood
1084 Neuroblastoma
17 Other
(also 191 Primates bodymap)
75 bp exon
75 bp exon
2824 bp [gt-ag] intron
10 GenBank accessions
1364 RNA-seq supporting reads
298 UHR pooled cells
121 Brain
50 Blood
871 Neuroblastoma
24 Other
(also 212 Primates bodymap)
239 bp exon
239 bp exon
496 bp [gt-ag] intron
14 GenBank accessions
420 RNA-seq supporting reads
152 UHR pooled cells
55 Brain
14 Blood
194 Neuroblastoma
5 Other
(also 69 Primates bodymap)
257 bp exon
257 bp exon
11 accessions, NM_031293.2
some from testis (seen 8 times)
capped 5' end, 4 accessions
Validated 3' end, 3 accessions
257 bp exon
173 bp exon
1008 bp [gt-ag] intron
5 GenBank accessions
1 RNA-seq supporting reads
1 Blood
(also 48 Primates bodymap)
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
277 bp [gt-ag] intron
4 GenBank accessions
44 RNA-seq supporting reads
9 UHR pooled cells
1 Brain
15 Blood
19 Neuroblastoma
(also 1 Primates bodymap)
116 bp exon
9911 bp [gt-ag] intron
4 GenBank accessions
53 RNA-seq supporting reads
19 UHR pooled cells
2 Brain
15 Blood
17 Neuroblastoma
(also 2 Primates bodymap)
249 bp exon
3381 bp [gt-ag] intron
10 GenBank accessions
295 RNA-seq supporting reads
84 UHR pooled cells
14 Brain
40 Blood
145 Neuroblastoma
12 Other
(also 218 Primates bodymap)
222 bp exon
222 bp exon
10025 bp [gt-ag] intron
10 GenBank accessions
320 RNA-seq supporting reads
105 UHR pooled cells
29 Brain
62 Blood
122 Neuroblastoma
2 Other
(also 107 Primates bodymap)
171 bp exon
1012 bp [gt-ag] intron
10 GenBank accessions
670 RNA-seq supporting reads
152 UHR pooled cells
49 Brain
83 Blood
371 Neuroblastoma
15 Other
(also 160 Primates bodymap)
111 bp exon
2469 bp [gt-ag] intron
11 GenBank accessions
769 RNA-seq supporting reads
181 UHR pooled cells
43 Brain
101 Blood
423 Neuroblastoma
21 Other
(also 186 Primates bodymap)
127 bp exon
87 bp [gt-ag] intron
11 GenBank accessions
652 RNA-seq supporting reads
114 UHR pooled cells
61 Brain
96 Blood
356 Neuroblastoma
25 Other
(also 192 Primates bodymap)
158 bp exon
3456 bp [gt-ag] intron
10 GenBank accessions
579 RNA-seq supporting reads
123 UHR pooled cells
38 Brain
92 Blood
307 Neuroblastoma
19 Other
(also 154 Primates bodymap)
244 bp exon
2025 bp [gt-ag] intron
9 GenBank accessions
651 RNA-seq supporting reads
148 UHR pooled cells
56 Brain
85 Blood
336 Neuroblastoma
26 Other
(also 155 Primates bodymap)
190 bp exon
175 bp [gt-ag] intron
8 GenBank accessions
676 RNA-seq supporting reads
167 UHR pooled cells
50 Brain
88 Blood
348 Neuroblastoma
23 Other
(also 144 Primates bodymap)
145 bp exon
979 bp [gt-ag] intron
9 GenBank accessions
790 RNA-seq supporting reads
173 UHR pooled cells
70 Brain
111 Blood
410 Neuroblastoma
26 Other
(also 62 Primates bodymap)
168 bp exon
271 bp [gt-ag] intron
9 GenBank accessions
668 RNA-seq supporting reads
180 UHR pooled cells
76 Brain
42 Blood
357 Neuroblastoma
13 Other
(also 79 Primates bodymap)
138 bp exon
2524 bp [gt-ag] intron
7 GenBank accessions
1013 RNA-seq supporting reads
225 UHR pooled cells
70 Brain
88 Blood
612 Neuroblastoma
18 Other
(also 155 Primates bodymap)
165 bp exon
562 bp [gt-ag] intron
10 GenBank accessions
1985 RNA-seq supporting reads
425 UHR pooled cells
106 Brain
125 Blood
1310 Neuroblastoma
19 Other
(also 238 Primates bodymap)
168 bp exon
303 bp [gt-ag] intron
11 GenBank accessions
1894 RNA-seq supporting reads
402 UHR pooled cells
134 Brain
125 Blood
1201 Neuroblastoma
32 Other
(also 144 Primates bodymap)
168 bp exon
1117 bp [gt-ag] intron
11 GenBank accessions
1753 RNA-seq supporting reads
401 UHR pooled cells
188 Brain
95 Blood
1044 Neuroblastoma
25 Other
(also 128 Primates bodymap)
104 bp exon
557 bp [gt-ag] intron
12 GenBank accessions
1713 RNA-seq supporting reads
358 UHR pooled cells
151 Brain
103 Blood
1084 Neuroblastoma
17 Other
(also 191 Primates bodymap)
75 bp exon
2764 bp [gt-ag] intron
2 GenBank accessions
229 RNA-seq supporting reads
17 UHR pooled cells
10 Brain
14 Blood
186 Neuroblastoma
2 Other
(also 18 Primates bodymap)
299 bp exon
496 bp [gt-ag] intron
14 GenBank accessions
420 RNA-seq supporting reads
152 UHR pooled cells
55 Brain
14 Blood
194 Neuroblastoma
5 Other
(also 69 Primates bodymap)
257 bp exon
9 accessions, NM_001160213.1
some from testis (seen 4 times)
brain (once), medulla (once)
capped 5' end, 2 accessions
Validated 3' end, 3 accessions
257 bp exon
56 bp exon
2752 bp [gt-ag] intron
2 GenBank accessions
52 RNA-seq supporting reads
7 UHR pooled cells
4 Brain
8 Blood
32 Neuroblastoma
1 Other
(also 2 Primates bodymap)
148 bp exon
2654 bp [gt-ag] intron
2 GenBank accessions
143 RNA-seq supporting reads
60 UHR pooled cells
3 Brain
27 Blood
52 Neuroblastoma
1 Other
(also 37 Primates bodymap)
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
131 bp exon
2 accessions
131 bp exon
44 bp exon
44 bp exon
10025 bp [gt-ag] intron
10 GenBank accessions
320 RNA-seq supporting reads
105 UHR pooled cells
29 Brain
62 Blood
122 Neuroblastoma
2 Other
(also 107 Primates bodymap)
171 bp exon
1012 bp [gt-ag] intron
10 GenBank accessions
670 RNA-seq supporting reads
152 UHR pooled cells
49 Brain
83 Blood
371 Neuroblastoma
15 Other
(also 160 Primates bodymap)
111 bp exon
2469 bp [gt-ag] intron
11 GenBank accessions
769 RNA-seq supporting reads
181 UHR pooled cells
43 Brain
101 Blood
423 Neuroblastoma
21 Other
(also 186 Primates bodymap)
127 bp exon
87 bp [gt-ag] intron
11 GenBank accessions
652 RNA-seq supporting reads
114 UHR pooled cells
61 Brain
96 Blood
356 Neuroblastoma
25 Other
(also 192 Primates bodymap)
158 bp exon
3456 bp [gt-ag] intron
10 GenBank accessions
579 RNA-seq supporting reads
123 UHR pooled cells
38 Brain
92 Blood
307 Neuroblastoma
19 Other
(also 154 Primates bodymap)
244 bp exon
2025 bp [gt-ag] intron
9 GenBank accessions
651 RNA-seq supporting reads
148 UHR pooled cells
56 Brain
85 Blood
336 Neuroblastoma
26 Other
(also 155 Primates bodymap)
190 bp exon
175 bp [gt-ag] intron
8 GenBank accessions
676 RNA-seq supporting reads
167 UHR pooled cells
50 Brain
88 Blood
348 Neuroblastoma
23 Other
(also 144 Primates bodymap)
145 bp exon
979 bp [gt-ag] intron
9 GenBank accessions
790 RNA-seq supporting reads
173 UHR pooled cells
70 Brain
111 Blood
410 Neuroblastoma
26 Other
(also 62 Primates bodymap)
168 bp exon
271 bp [gt-ag] intron
9 GenBank accessions
668 RNA-seq supporting reads
180 UHR pooled cells
76 Brain
42 Blood
357 Neuroblastoma
13 Other
(also 79 Primates bodymap)
138 bp exon
87 bp [gt-ag] intron
1 GenBank accession
48 RNA-seq supporting reads
29 UHR pooled cells
1 Brain
10 Blood
8 Neuroblastoma
(also 11 Primates bodymap)
193 bp exon
193 bp exon
2244 bp [gt-ag] intron
1 GenBank accession
12 RNA-seq supporting reads
9 UHR pooled cells
1 Brain
1 Blood
1 Neuroblastoma
165 bp exon
562 bp [gt-ag] intron
10 GenBank accessions
1985 RNA-seq supporting reads
425 UHR pooled cells
106 Brain
125 Blood
1310 Neuroblastoma
19 Other
(also 238 Primates bodymap)
168 bp exon
303 bp [gt-ag] intron
11 GenBank accessions
1894 RNA-seq supporting reads
402 UHR pooled cells
134 Brain
125 Blood
1201 Neuroblastoma
32 Other
(also 144 Primates bodymap)
1 accession from testis
15 bp exon
197 bp exon
197 bp exon
30 bp uORF
197 bp exon
1008 bp [gt-ag] intron
5 GenBank accessions
1 RNA-seq supporting reads
1 Blood
(also 48 Primates bodymap)
72 bp exon
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
153 bp exon
10304 bp [gt-ag] intron
19 GenBank accessions
667 RNA-seq supporting reads
117 UHR pooled cells
56 Brain
132 Blood
346 Neuroblastoma
16 Other
(also 262 Primates bodymap)
201 bp exon
2 accessions, some from testis (seen 2 times)
capped 5' end, 2 accessions
201 bp exon
87 bp exon
1117 bp [gt-ag] intron
11 GenBank accessions
1753 RNA-seq supporting reads
401 UHR pooled cells
188 Brain
95 Blood
1044 Neuroblastoma
25 Other
(also 128 Primates bodymap)
104 bp exon
557 bp [gt-ag] intron
12 GenBank accessions
1713 RNA-seq supporting reads
358 UHR pooled cells
151 Brain
103 Blood
1084 Neuroblastoma
17 Other
(also 191 Primates bodymap)
75 bp exon
10068 bp [gt-ag] intron
2 GenBank accessions
31 RNA-seq supporting reads
14 UHR pooled cells
2 Blood
15 Neuroblastoma
676 bp exon
3 accessions, some from blood (seen 2 times)
natural killer cells
cell line (2), lung tumor (once)
676 bp exon
164 bp exon
164 bp exon
42 bp uORF
164 bp exon
464 bp [gt-ag] intron
1 GenBank accession
72 bp exon
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
153 bp exon
10304 bp [gt-ag] intron
19 GenBank accessions
667 RNA-seq supporting reads
117 UHR pooled cells
56 Brain
132 Blood
346 Neuroblastoma
16 Other
(also 262 Primates bodymap)
166 bp exon
166 bp exon
1 accession from testis
capped 5' end, 1 accession
166 bp exon
49 bp exon
785 bp [gt-ag] intron
16 GenBank accessions
72 bp exon
72 bp exon
6280 bp [gt-ag] intron
25 GenBank accessions
236 RNA-seq supporting reads
49 UHR pooled cells
8 Brain
66 Blood
111 Neuroblastoma
2 Other
(also 158 Primates bodymap)
153 bp exon
277 bp [gt-ag] intron
4 GenBank accessions
44 RNA-seq supporting reads
9 UHR pooled cells
1 Brain
15 Blood
19 Neuroblastoma
(also 1 Primates bodymap)
116 bp exon
9911 bp [gt-ag] intron
4 GenBank accessions
53 RNA-seq supporting reads
19 UHR pooled cells
2 Brain
15 Blood
17 Neuroblastoma
(also 2 Primates bodymap)
153 bp exon
1 accession from testis
capped 5' end, 1 accession
153 bp exon
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Read more...
Mouse over the ending of each transcript gives tissues from which the supporting cDNAs were extracted. Details on tissue of origin for each intron and exon is available from the
intron and exons table .
Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. Names not underlined result from cDNA concatenation in the coding region and should be experimentally checked.
Introns are depicted by broken lines; the height of the top of each intron reflects the relative number of clones supporting this intron.
]^[ A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron).
] ^ ] A blue broken line denotes non-standard introns, exactly supported, but with non-standard at-ac or any other boundaries.
]-[ Pink and
] - ] blue straight lines represent 'fuzzy' introns of the standard and non-standard types respectively, those introns do not follow the 16 bp rule. Black straight lines ]-[denote gaps in the alignments.
Exons: Wide filled pink areas represent putative protein coding regions, narrow empty pink boxes represent the 5'UTR (on the left) and 3' UTR (on the right). Flags identify validated endings: cap site on the 5' side, polyadenylation site on the 3' side. Filled flags correspond to frequent events while empty flags have lesser supporting cDNAs (yet all are validated); at the 3' side, black flags are associated to the main AATAAA signal,
blue flags to any single letter variant of the main . More explanations are given in the
gene help file
