Gene XKR5TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
Compact gene diagram
According to AceView, this gene is expressed at low level
, only 6.5% of the average gene in this release. The sequence
of this gene is defined by 8 GenBank accessions
, some from neuroblastoma cot 10-normalized (seen 4 times), brain (2), neuroblastoma cells (2). We annotate structural defects or features
in one cDNA clone.
Alternative mRNA variants and regulation:
The gene contains 12 distinct introns
(10 gt-ag, 2 gc-ag). Transcription produces 3 alternatively spliced mRNAs
. There are 2 non overlapping alternative last exons and 2 validated alternative polyadenylation sites
(see the diagram
). The mRNAs appear to differ by presence or absence of 3 cassette exons
. 209 bp of this gene are antisense to spliced gene zerla
, raising the possibility of regulated alternate expression.
Note that mRNA .cAug10 was found in vivo
, although it is a predicted target of nonsense mediated mRNA decay
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).
There is one article
specifically referring to this gene in PubMed. Proteins are expected to localize
in various compartments (endoplasmic reticulum membrane, integral to membrane). No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential:
The 3 spliced mRNAs putatively encode good proteins
, altogether 3 different isoforms (3 complete
), some containing XK-related protein domain
[Pfam], some transmembrane domains [Psort2]
2 isoforms are annotated using as Met a Kozak-compatible
non-AUG start, thereby gaining a minimum of 75 amino acids N-terminal to the first AUG. Finally proteins from this gene may be modulated by acetylation; phosphorylation
, as detailed at PhosphoSite.
Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12
8 supporting clones for gene XKR5
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.
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.
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.
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
Links to the sequence
most 5' clones
(with AA variation)
relative to genome
|AY534242 || ||.a ||1 to 4889 ||1 to 4888 ||M69V V291W D292T Q293S P294L ... ||tiling clone, AAA || ||4888/4888 |
| 2 diff|
|NM_207411.4 || ||.a ||1 to 4889 ||1 to 4888 ||V291W D292T Q293S P294L A295Q ... ||RefSeq, AAA || ||4888/4888 |
| 1 diff|
|AY358489 || ||.a ||130 to 2745 ||1 to 2615 ||M69V V291W D292T Q293S P294L ... || || ||2615/2615 |
| 3 diff|
|AY534243 || ||.b ||1 to 4881 ||1 to 4880 ||E6K V202W D203T Q204S P205L ... ||tiling clone, AAA || ||4880/4880 |
| 4 diff|
|CR604676 ||Neuroblastoma Cot 10-normalized ||.c ||1 to 2086 ||1 to 2085 ||V176F T177S F178L Y179A M180R ... ||tiling clone, || ||2086/2085 |
| 6 diff|
|AL521639 ||brain, neuroblastoma cells, Neuroblastoma Cot 10-normalized ||.c ||1 to 908 ||1 to 907 || || || ||907/907 |
| 5 diff|
|AL521638 ||brain, neuroblastoma cells, Neuroblastoma Cot 10-normalized ||.c ||1121 to 2086 ||965 to 1 || || || ||965/965 |
| 2 diff|
|BX368984 ||Neuroblastoma Cot 10-normalized ||Gene XKR5, variant not shown || || || || ||This clone was ignored || || |