DreINT0083214 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1124902-1126652:-
Coord C1 exon
chr24:1126414-1126652
Coord A exon
chr24:1125125-1126413
Coord C2 exon
chr24:1124902-1125124
Length
1289 bp
Sequences
Splice sites
5' ss Seq
GAGGTACAG
5' ss Score
6.62
3' ss Seq
GCACTGTTGTTGTCCTGCAGGTC
3' ss Score
11.27
Exon sequences
Seq C1 exon
GTGTAATAAGGGTCGTGTGGGTCGTCAGTGTGAGTGCCGGAAGGATGAAGTGTCCACCGAGGATCTGGACAAGAACTGCCGCAAAGACAACGGCACCGACATCTGCAGCAACAACGGCGAGTGTGTGTGCGGGACCTGCGAATGCAAGAAGCGGGAGAATCCAGAGGAGCGATACAGCGGGAAATACTGCGAGTGCGACAACTTCAACTGCGACCGCTCCAACAACAAACTCTGCGGAG
Seq A exon
GTACAGGACCACTTACACTGTCCTGTTCACAGAAATACATGCAGTACTGCTGGCTGAGTCAGTGACAGAGGAGTCATTTCATTACTTATCAACTAGAAAATGTCAAGTAGGAGAAGTACTGTTCATTTTTAGGTTGCTTAATTGCAGTTAATTATGATGTGCCCATCGTAAATATGGTAAATAAATTCAGCAGTTCTGTATAAATCAAAGAAGCTGAGGAATTGTACAAAGAAGGTCACATTTGGCAAGACGATTTAGAAACAATGAGTTGAGTCAGAATTTAATGATTAATGCTGGTGAAAAATAGTTTGTGTTTTCATTTCTACTACACTGCCTGAGATAGCTGAATTTACTGTTTGATTAGATAAATTACACAAGCTGGATTCACTGGTCAGATGAGCTAGAAATGCAGCACACTGAGGACATCTGCTGGTTATAAGGGGTTAATGCAATAAGACAAGCATAAACTAAAACTAATCAGATTGTTATCGATTGCTGTGTGGACACAAATATAGTTGTCATTATAGTTATAGTTAGAATTATCATCTGTATAATTATCATCAATGATTTATACTTCAGTTTTGATTTAAGGTAGACTAATTGTGATTTCAGTGGGACTTTAATTTTGTATTTCAGTGAGATTTGGACTTCAGAGGACTTTAACTTTGATTTCAGTAGGACTATTATTTTGATTTCCGTGGGACTTTTATTTAGGTTTTACTGGGACTTTTATTTTGATTTCAGTGGGACTTTAATTTTGGATTTCAGTGAGATTTTGACTTCAGAGGACTTTGATTTTAGTGGGACTTTTATTTTGATTTCAGTGGGACTTTAATTTTGGATTTCAGTGAGATTTTGACTTCAGATGACTTTGATTTCAGTGGGACTTTTATTTTGATTTCAGTGGGACTTTTATTTTGATTTCAGTGGGACTTTAATTTTGATTTCAGTGGGACTTTAATTTTGATTTCAGTGAAATATTTCCTTCAGAGGCCTTTAATTTTAATTTCACTGGGACTTTTATTTTGATATCAGTGGGACTTTAATTTTGATTTCACTGGTACTTTTATTTTGATATCAGTGTGACTTTAATTTTGATTTCAGTGGGACTTTAATTTTGTATTTTAGTGTAATTTTGACTTCAGAGGACTTTAATTTTGATTTCAAGGTAATTTTGATTTCAGATAGATTTAGCGGTCATCTAATTTAGATTTTTATACCACTGGTGTGAGCAGCTCTGAACACTGAGCACATGCTAATATAATAACAGCACTGTTGTTGTCCTGCAG
Seq C2 exon
GTCACGGCCGCTGTGAGTGCAGGGTGTGTGTGTGCGACGCCAACTACACAGGCAGCGCCTGCGACTGCTCCCTCGACACCTCCACCTGTCTGGCCTCCAACAAGCAGATCTGCAACGGCCGGGGGATCTGTGAGTGCGGGACCTGCAGGTGCACAGACCCCAAGTTCCAAGGGCCCACCTGCGAGATCTGCCCCACCTGCCCCGGAGTCTGCACCGAACACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079748=EGF_2=WD(100=46.9),PF079748=EGF_2=PU(32.3=12.3)
A:
NA
C2:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCTGGACAAGAACTGCCG
R:
CCTTGGAACTTGGGGTCTGTG
Band lengths:
351-1640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]