DreALTA0019670-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000070818 | pax7b
Description
paired box 7b [Source:ZFIN;Acc:ZDB-GENE-080917-54]
Coordinates
chr23:20938263-20938822:+
Coord C1 exon
chr23:20938263-20938407
Coord A exon
chr23:20938694-20938697
Coord C2 exon
chr23:20938698-20938822
Length
4 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
CCTTTTTATTATCCCATCAGTAA
3' ss Score
5.71
Exon sequences
Seq C1 exon
CAGGTGGCAACACCTGACGTGGAAAAACGAATTGAGGAATACAAGCGCGAAAATCCCGGCATGTTTAGTTGGGAGATCCGAGACAAACTGTTGAAGGACGGGGTGTGTGACAGAAGTACAGTTCCCTCAGGTGAGGCCTCATCTG
Seq A exon
TAAG
Seq C2 exon
TTCTATCAGCCGGGTTCTTCGTGCGCGTTTCGGCAAAAAAGACGACGAGGATGATTGTGACAAAAAAGATGACACTGGAGAGAAAAAAACGAAACACAGTATTGACGGCATTCTGGGAGACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000070818-6-4,6-3-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.932
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(36.6=100)
A:
NA
C2:
PF0029213=PAX=PD(6.1=18.2)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAGATCCGAGACAAACTGT
R:
ACGAAGAACCCGGCTGATAGA
Band lengths:
98-102
Functional annotations
There are 1 annotated functions for this event
PMID: 15688409
Four isoforms due to 3nt (Q, HsaALTA1001031) and 6nt (GL, HsaALTA1001032) insertions/deletion. The relative DNA binding affinity for each isoform is: Q-GL- > Q+GL- > Q-GL+ >/= Q+GL+ for class I sites and Q-GL-, Q+GL- > Q-GL+, Q+GL+ for class II sites. This results in different transcriptional activity.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]