Mus musculus gene Tsr1, encoding TSR1, 20S rRNA accumulation, homolog (yeast).
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Mus musculus cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 3.5 times the average gene in this release. The sequence of this gene is defined by 392 GenBank accessions from 346 cDNA clones, some from visual cortex (seen 16 times), whole body (16), embryonic stem cell (13), blastocyst (12), eye (10), mammary (10), pancreas (10) and 71 other tissues. We annotate structural defects or features in 8 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 18 distinct introns (17 gt-ag, 1 gc-ag). Transcription produces 10 different mRNAs, 8 alternatively spliced variants and 2 unspliced forms. There are 3 non overlapping alternative last exons and 2 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 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 4 introns. 3271 bp of this gene are antisense to spliced gene Srr, raising the possibility of regulated alternate expression.
3 variants were isolated in vivo, despite the fact that they are predicted targets of nonsense mediated mRNA decay (NMD).
Function: There is one article specifically referring to this gene in PubMed. No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_2144566 for in depth functional annotation of this gene.
Protein coding potential: The 8 spliced and 2 unspliced mRNAs putatively encode good proteins, altogether 10 different isoforms (7 complete, 1 COOH complete, 2 partial), some containing domains AARP2CN, Protein of unknown function DUF663 [Pfam], a coiled coil stretch [Psort2].
Isoform Tsr1.cSep07 is annotated using as Met a Kozak-compatible a..AAG. start, thereby gaining 75 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 11, links to other databases and other names
Map: This gene Tsr1 maps on chromosome 11, at 11 B5 according to Entrez Gene. In AceView, it covers 12.08 kb, from 74710771 to 74722848 (NCBI 37a, Aug 2007), on the direct strand.
Links to: manual annotations from MGI_2144566, the SNP view, gene overviews from Gene 104662, expression data from Gene 104662, molecular and other annotations from UCSC.
Other names: The gene is also known as Tsr1, AU040765, AW550801, mKIAA1401 or RP23-174M12.4, LOC104662.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene TSR1 (e=2 10-76).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene 2F3 (e=8 10-47).
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G42440 (e=2 10-35)
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene Tsr1 5' 3' encoded on plus strand of chromosome 11 from 74,710,771 to 74,722,848 a [NM] b c g d e f h i-u j-u 1 2kb 0 136 bp exon 136 bp exon 161 bp [gt-ag] intron 121 GenBank accessions 104 bp exon 701 bp [gt-ag] intron 118 GenBank accessions 220 bp exon 107 bp [gt-ag] intron 88 GenBank accessions 135 bp exon 509 bp [gt-ag] intron 51 GenBank accessions 425 bp exon 911 bp [gt-ag] intron 31 GenBank accessions 160 bp exon 360 bp [gt-ag] intron 31 GenBank accessions 158 bp exon 1653 bp [gt-ag] intron 35 GenBank accessions 194 bp exon 815 bp [gt-ag] intron 34 GenBank accessions 163 bp exon 214 bp [gt-ag] intron 37 GenBank accessions 111 bp exon 574 bp [gt-ag] intron 36 GenBank accessions 133 bp exon 1311 bp [gt-ag] intron 28 GenBank accessions 117 bp exon 372 bp [gt-ag] intron 30 GenBank accessions 141 bp exon 81 bp [gt-ag] intron 25 GenBank accessions 75 bp exon 107 bp [gt-ag] intron 30 GenBank accessions 1115 bp exon 162 accessions, NM_177325 some from blastocyst (seen 10 times) whole embryo including extraembryonictissues at 8.5-days postcoitum (8) pancratic islet (7), upper head (7) whole body (7) Validated 3' end, 60 accessions 1115 bp exon 109 bp exon 109 bp exon 161 bp [gt-ag] intron 121 GenBank accessions 104 bp exon 701 bp [gt-ag] intron 118 GenBank accessions 220 bp exon 107 bp [gt-ag] intron 88 GenBank accessions 135 bp exon 509 bp [gt-ag] intron 51 GenBank accessions 425 bp exon 911 bp [gt-ag] intron 31 GenBank accessions 160 bp exon 360 bp [gt-ag] intron 31 GenBank accessions 158 bp exon 1653 bp [gt-ag] intron 35 GenBank accessions 194 bp exon 815 bp [gt-ag] intron 34 GenBank accessions 163 bp exon 214 bp [gt-ag] intron 37 GenBank accessions 111 bp exon 574 bp [gt-ag] intron 36 GenBank accessions 133 bp exon 1311 bp [gt-ag] intron 28 GenBank accessions 117 bp exon 372 bp [gt-ag] intron 30 GenBank accessions 141 bp exon 83 bp [gt-ag] intron 1 GenBank accession 73 bp exon 73 bp exon 107 bp [gt-ag] intron 30 GenBank accessions 1 accession from mammary tumor metastatized to lung.mmtv-ltr/wnt1 model. expression driven by an mmtv-ltrenhancer Validated 3' end, 1 accession 1111 bp exon 146 bp exon 146 bp exon 966 bp [gt-ag] intron 2 GenBank accessions 220 bp exon 107 bp [gt-ag] intron 88 GenBank accessions 135 bp exon 509 bp [gt-ag] intron 51 GenBank accessions 425 bp exon 911 bp [gt-ag] intron 31 GenBank accessions 160 bp exon 360 bp [gt-ag] intron 31 GenBank accessions 158 bp exon 1653 bp [gt-ag] intron 35 GenBank accessions 194 bp exon 815 bp [gt-ag] intron 34 GenBank accessions 163 bp exon 214 bp [gt-ag] intron 37 GenBank accessions 62 bp exon 623 bp [gc-ag] intron 1 GenBank accession 133 bp exon 9 accessions, some from 4-cell stage embryo (seen 5 times) brain (2), pituitary gland (2) whole brain (2) 133 bp exon 166 bp exon 372 bp [gt-ag] intron 30 GenBank accessions 141 bp exon 81 bp [gt-ag] intron 25 GenBank accessions 75 bp exon 107 bp [gt-ag] intron 30 GenBank accessions 130 bp exon 2 accessions, some from embryo (seen once) skin (once), whole embryo (once) 130 bp exon 947 bp exon 947 bp exon 161 bp [gt-ag] intron 121 GenBank accessions 104 bp exon 701 bp [gt-ag] intron 118 GenBank accessions 220 bp exon 107 bp [gt-ag] intron 88 GenBank accessions 135 bp exon 509 bp [gt-ag] intron 51 GenBank accessions 425 bp exon 911 bp [gt-ag] intron 31 GenBank accessions 678 bp exon 678 bp exon 1653 bp [gt-ag] intron 35 GenBank accessions 194 bp exon 1192 bp [gt-ag] intron 1 GenBank accession 111 bp exon 574 bp [gt-ag] intron 36 GenBank accessions 133 bp exon 1311 bp [gt-ag] intron 28 GenBank accessions 117 bp exon 372 bp [gt-ag] intron 30 GenBank accessions 141 bp exon 81 bp [gt-ag] intron 25 GenBank accessions 75 bp exon 107 bp [gt-ag] intron 30 GenBank accessions 105 accessions, some from whole body (seen 9 times) embryonic stem cell (8) activated spleen (6) eye (5), whole eye (5) 400 bp exon 126 bp exon 126 bp exon 161 bp [gt-ag] intron 121 GenBank accessions 104 bp exon 701 bp [gt-ag] intron 118 GenBank accessions 220 bp exon 107 bp [gt-ag] intron 88 GenBank accessions 135 bp exon 509 bp [gt-ag] intron 51 GenBank accessions 514 bp exon 5 accessions, some from infiltrating ductal carcinoma (seen once) mammary (once) 514 bp exon 107 bp exon 107 bp exon 574 bp [gt-ag] intron 36 GenBank accessions 133 bp exon 1311 bp [gt-ag] intron 28 GenBank accessions 117 bp exon 372 bp [gt-ag] intron 30 GenBank accessions 297 bp exon 297 bp exon 107 bp [gt-ag] intron 30 GenBank accessions 2 accessions, some from mammary (seen once) tumor, gross tissue (once) 116 bp exon 110 bp exon 110 bp exon 161 bp [gt-ag] intron 121 GenBank accessions 104 bp exon 701 bp [gt-ag] intron 118 GenBank accessions 394 bp exon 3 accessions, some from 8-cell stage embryo (seen 3 times) 394 bp exon 1235 bp exon 1235 bp exon 57 accessions, some from visual cortex (seen 12 times) amnion (5), testis (4) rathke's pouches (3) head (2) 1235 bp exon 870 bp exon 870 bp exon 11 accessions, some from corpora quadrigemina (seen 4 times) cerebellum (once), eye (once) peritubular cells (once) pituitary gland (once) 870 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.
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Sequences: click on the numbers to get the DNA back to top


Click on the headers to reorder the lines
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aSep07 3387 bp 803 aa 39 bp 936 bp 2409 bp 2kb probably including promoter 11263 bp 1kb
bSep07 3354 bp 724 aa 12 bp 1167 bp 2172 bp 2kb probably including promoter 11232 bp 1kb
cSep07 1796 bp 528 aa 89 bp 120 bp   2kb possibly including promoter 7954 bp 1kb
dSep07 3680 bp 382 aa 850 bp 1681 bp   2kb possibly including promoter 11359 bp 1kb
eSep07 1099 bp 356 aa 29 bp   1068 bp 2kb probably including promoter 2577 bp 1kb
fSep07 770 bp 191 aa   192 bp   2kb 3134 bp 1kb
gSep07 512 bp 170 aa     510 bp 2kb 1072 bp 1kb
hSep07 608 bp 141 aa 13 bp 169 bp 423 bp 2kb probably including promoter 1470 bp 1kb
iSep07-unspliced 1235 bp 77 aa 915 bp 86 bp   2kb possibly including promoter 1235 bp 1kb
jSep07-unspliced 870 bp 57 aa 89 bp 607 bp   2kb possibly including promoter 870 bp 1kb
Gene neighbors and Navigator on chromosome 11 B5 back to top
C C C E130309D14Rik C R P 1300001I01Rik C R P C Mett10d C R Mnt D C R P C Tsr1 C R P C R Smg6 C R P C G R Rtn4rl1 D C R P R Smyd4 C R P C R P Garnl4 D C R P Pafah1b1 C R P Sgsm2 R C R P Srr G C G C D C R P Hic1 D C R P Dph1andRP23-143A14.5 D C R P Rpa1 C 100kb 0 sposu, 3 accessions RVT_1.217, 1 accession spawsu, 2 accessions E130309D14Rik, 120 accessions 4 variants 1300001I01Rik, 517 accessions 11 variants stusu, 1 accession Mett10d, 277 accessions 13 variants Mnt, 160 accessions, 4 variants swarsu, 2 accessions Tsr1, 364 accessions, 10 variants rekiho, 2 accessions rokiho, 14 accessions Smg6, 246 accessions, 14 variants duso, 3 accessions LOC668604, 27 accessions 3 variants Rtn4rl1, 108 accessions charrar, 2 accessions Smyd4, 109 accessions 9 variants snorsu, 1 accession makaho, 4 accessions mikaho, 1 accession spasu, 1 accession mokaho, 2 accessions speesu, 1 accession spersu, 3 accessions, 2 variants speysu, 1 accession hikaho, 1 accession hukaho, 11 accessions hekaho, 1 accession spoysu, 1 accession nikaho, 1 accession nukaho, 4 accessions tikaho, 9 accessions tukaho, 4 accessions tokaho, 2 accessions starsu, 2 accessions charar, 17 accessions stawsu, 3 accessions steesu, 5 accessions stersu, 1 accession stoysu, 2 accessions sekaho, 12 accessions sokaho, 1 accession kikaho, 6 accessions swysu, 1 accession chyrar, 1 accession kukaho, 1 accession swosu, 3 accessions wakiho, 1 accession sweesu, 1 accession rikiho, 2 accessions yukiho, 3 accessions makiho, 3 accessions sworsu, 2 accessions mukiho, 3 accessions swoysu, 1 accession baso, 1 accession byso, 1 accession buso, 2 accessions mokiho, 1 accession hikiho, 3 accessions boso, 4 accessions hukiho, 1 accession hekiho, 2 accessions barso, 1 accession bawso, 1 accession beeso, 5 accessions, 2 variants hokiho, 2 accessions berso, 2 accessions borso, 2 accessions nakiho, 2 accessions nikiho, 7 accessions, 2 variants boyso, 1 accession daso, 2 accessions doso, 1 accession darso, 2 accessions nekiho, 1 accession dawso, 1 accession nokiho, 5 accessions takiho, 2 accessions deyso, 3 accessions dorso, 1 accession doyso, 1 accession faso, 2 accessions fuso, 3 accessions tekiho, 5 accessions farso, 1 accession ferso, 1 accession feyso, 1 accession tokiho, 1 accession guso, 1 accession garso, 1 accession gawso, 1 accession yokaho, 2 accessions snoysu, 1 accession mukaho, 7 accessions mekaho, 5 accessions spysu, 1 accession hakaho, 2 accessions spusu, 1 accession sparsu, 2 accessions sporsu, 1 accession hokaho, 2 accessions nakaho, 10 accessions 2 variants stasu, 1 accession stysu, 4 accessions nekaho, 3 accessions nokaho, 6 accessions takaho, 16 accessions stosu, 7 accessions tekaho, 1 accession sakaho, 4 accessions sikaho, 2 accessions sukaho, 1 accession steysu, 4 accessions storsu, 1 accession kakaho, 3 accessions swasu, 1 accession swusu, 3 accessions, 2 variants kekaho, 6 accessions kokaho, 1 accession swawsu, 3 accessions, 2 variants swersu, 3 accessions rukiho, 2 accessions sweysu, 2 accessions yakiho, 2 accessions yokiho, 7 accessions mikiho, 1 accession mekiho, 1 accession hakiho, 2 accessions kinahe, 1 accession beyso, 5 accessions dyso, 1 accession nukiho, 1 accession deeso, 2 accessions derso, 1 accession tikiho, 2 accessions churar, 12 accessions fyso, 2 accessions foso, 1 accession tukiho, 3 accessions fawso, 2 accessions chorar, 2 accessions feeso, 2 accessions forso, 3 accessions foyso, 1 accession sakiho, 1 accession gaso, 4 accessions gyso, 1 accession sikiho, 10 accessions goso, 3 accessions Garnl4, 450 accessions 13 variants Pafah1b1, 423 accessions 11 variants Sgsm2, 160 accessions 9 variants rakiho, 3 accessions Srr, 329 accessions, 15 variants LOC100043429, 115 accessions LOC627835, 21 accessions Hic1, 68 accessions, 2 variants Dph1andRP23-143A14.5, 224 accessions 8 variants Rpa1, 310 accessions, 7 variants rve.121, 1 accession ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               1 article in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u, .j-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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