DreINT0083223 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1130852-1132072:-
Coord C1 exon
chr24:1131917-1132072
Coord A exon
chr24:1130948-1131916
Coord C2 exon
chr24:1130852-1130947
Length
969 bp
Sequences
Splice sites
5' ss Seq
TACGTATGT
5' ss Score
5.54
3' ss Seq
TTCTTTCCTCTCTCGACTAGGAT
3' ss Score
9.85
Exon sequences
Seq C1 exon
GAGCACATTGGCTGGAGAAACGTCACCCGTTTGTTGGTTTTCTCTACTGACGCAGGTTTTCATTTTGCTGGAGATGGGAAACTCGGAGGAATTGTGCTTCCCAATGATGGGAGGTGTCACTTAGAAAATGACATGTACACCATGAGCCATTATTAC
Seq A exon
GTATGTATACGATTGAGCTAATACACTGTCATCATTATAATTAGCGTTATATTTGAAGGAATTGAAGGGAAAAGGTGGAAGTAAAATATGCATTAGATACATTTTTTATCAATTAAATATATTTTTATTTGTTGTTTAGTTTTGTTGTTTTATTTGTTTTTATTAGTTTATTTGTTAAATTGTATTTGTTTTTAACTGCAAAAGCAGTCATTTTCAATTCTTTTAATCATTAGTGACTAATAAGTGACTTTTAATCGTAGGTGGTTTGTATTGCTTTTATTAGTCTAGAAGCAATATCGCTGCTTTTGACTTTTATTTGCAAAGTATTTAATGATTAATAATTTGCTAATATTAAGCATGCACAAGTACTATTTTTTCATTTATGTTTTTATTACATTTTTTGTAGTTTGCAGAGTTATTTATTATTAACAATTTGTTATCATTAATTTTGCGAATATTAAACACACAAAAATGTTTTTTCTATTTTAGATTGTATTTTTATTACAATTTTTTGTAGTTTTAAAATATATTATTATATTTGTTTATATCTGTAATTTATATTTTTATTTTATTTTTATAGCTTTTTAAATATGTCTATATAATTTGTTTGATTGTTTTTATTAAGTAATTTTCTGTTAAATTTTAGTTATTATGGCACAATTAAAGACAAATATTTCCATATAACATAAAAAAAATTTGTTAATGTTTATTTAAGTAATAATTATATAATCTATGATGATTTAAATATCCAGTTCAAGTATCTTAAAGCCCAAGTATATCATATTCAATTACAAATTAAATTATTCAAGTAAATATTTTGGCCTGTTTATATTCTCTACCTTCAATAGTTTGCATGAGTATTGCCTATAATGTTTACATTCCTGTCTTCAGATAATTTTAATACCAGACTGTTGGATGTTTGACAGATTTAGCATAACTTTCATTTCTTTTCTTTCCTCTCTCGACTAG
Seq C2 exon
GATTACCCCTCGATCGCCCACTTGGTTCAGAAACTGAGTGAAAACAACATCCAGACCATCTTCGCTGTTACAGAAGAGTTTCAGCCTGTATATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:7
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:
PF0036213=Integrin_beta=FE(11.8=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(7.2=100)
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:
AGCACATTGGCTGGAGAAACG
R:
ATACAGGCTGAAACTCTTCTGT
Band lengths:
246-1215
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]