DreALTA0019669-1/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000070818 | pax7b
Description
paired box 7b [Source:ZFIN;Acc:ZDB-GENE-080917-54]
Coordinates
chr23:20937786-20938392:+
Coord C1 exon
chr23:20937786-20938021
Coord A exon
NA
Coord C2 exon
chr23:20938266-20938392
Length
0 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TAAATCAAACACAAAAGCAGGTG
3' ss Score
-1.13
Exon sequences
Seq C1 exon
TTTCAACTCCTTTGGGCCAAGGTCGAGTGAATCAGCTTGGCGGTGTATTCATCAATGGCAGGCCTTTGCCAAATCATATCCGCCACAAAATTGTTGAAATGGCTCACCACGGCATCCGTCCCTGCGTGATCTCAAGACAGCTTCGCGTTTCCCATGGCTGCGTGTCCAAAATCCTCTGCCGGTATCAAGAAACTGGCTCAATCCGTCCTGGAGCAATAGGAGGAAGTAAACCTAGA
Seq A exon
NA
Seq C2 exon
GTGGCAACACCTGACGTGGAAAAACGAATTGAGGAATACAAGCGCGAAAATCCCGGCATGTTTAGTTGGGAGATCCGAGACAAACTGTTGAAGGACGGGGTGTGTGACAGAAGTACAGTTCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000070818-4-2,4-1-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.241 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(55.7=92.4)
A:
NA
C2:
PF0029213=PAX=FE(36.6=100)
Main Inclusion 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:
CGTCCTGGAGCAATAGGAGGA
R:
CTCCCAACTAAACATGCCGGG
Band lengths:
105-108
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]