DreINT0083213 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1126414-1128189:-
Coord C1 exon
chr24:1127987-1128189
Coord A exon
chr24:1126653-1127986
Coord C2 exon
chr24:1126414-1126652
Length
1334 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GTGTGTTGGTGTGTGTTCAGGTG
3' ss Score
8.12
Exon sequences
Seq C1 exon
GTGTCGTTCAACATTAACATCACGGCTCAAGGCTGCCCTAAACAAGGCAAGACAGAGACCATAAAGATCAAGCCGCTGGGCTTCACTGAGGAGGTGGAGATAACACTGAGCTTCATCTGCGAATGCGAATGCCACAAACACGCCATGAAGAACAGCCCGCTGTGCCACAACGGCAATGGCTCCTTTGAGTGCGGAGCCTGCAG
Seq A exon
GTGAGAAAAACACACGTCTTTGGTCAGTTATGTTAAGTCTAAAGTGCAGTTGAAGACAATATTATTAGCCAAGAGCTGCAGAATTCAGGCTAATGTTAGCAAACCACCAAGAAGAACCACATCCAGCAGGAGTAACTGTGGACGCCAGGGGAAGCTGCCTAAAGGGTTGTCTGGCTGCTGACCCCGATTGTATTCAAAAAGCATGCAAGCACAGCTTAACGTGCACCTCAGCTCTCCTGTTTCCACCAAAACGGTTGGTCTGGAGCTCCACAGGGTCAATATACATGGCTGAGCTGCTATAGCCAAAGCTTTGGTTACTCTTGCTAATGCCAAACGCTGGTTTAAATGTTGCCAGCAGCAAAAATTTTGGGCTGTGGACAAGGTGAAACATGTAATGTTCTTTAATGAGTCCACCTCCATTGTCTTTCCCACATCTGAGAGAGTTACAGTGTGGAGAAGCCCCAAAAAAGCGTCCCACTCAGACCGCTGATGCCCAGAGTGTTGGTCTGGAGCTCCACAGGGTTAATAAACATGGCTGAGCTGCTATAGCCAAACCTTTGGTCACTCGTGCCAATTCCAAACGCCGGTTTCAATAGTGTCCACAGCGAAAATCTTGGGCTTTTGACAATGTGAAACATGTAATGTTCTCTAATGAGTCCACCTTCATTGTCTTTCCCACATCTGAGAGAGATACAGTGTGGAGAAGCCCCAAAGAAGCGTCCCACCCAGACTGCTGATGCCCAGAGTGAAGCATGTGGGGGATCAGTGATGGTTTGGGCTTCAATAACATGGCATTCCCTTGGCCCAATACTGGTGCTAGATTAGGGTCACTGCCAAGGACTGCCAAACCGTTCTGGAGGACCATGTGACCCAATAGTTAAAACACTGCATCCTGAAGGCGGTGCTGTGTATCAGGATGATAATGCACCAATATACACAGCAAGACTGTTGACAGAGTATATGATATATACTGCTTGCTTCAACCTTAACTCCTGCACAATATTCATCTTTAATACCTCTCTTGCACAATATCCTGCGCAACATTGTTCAGTCTCATGTAAAAGTACTTGTATAGTCTTATGTGTGTAGTTAAGTATGTTATAGTATATGTTAGTTATGCATCGTTTTTTATAGTAGCTCTTATGTCCAGTGTTGTGTTTGTATTTATGATTACTTTATGTAGCACTGTTGTCCTGATAGACACAACATTTCGTTCCTCTGTACGTCCACACATGCAGCAGTATGACAATAATGTTTGACTTGATATATATGGACAAATTATTTGCTTTAATATGTTTAAAAATGATATAATGTGTGTGTTGGTGTGTGTTCAG
Seq C2 exon
GTGTAATAAGGGTCGTGTGGGTCGTCAGTGTGAGTGCCGGAAGGATGAAGTGTCCACCGAGGATCTGGACAAGAACTGCCGCAAAGACAACGGCACCGACATCTGCAGCAACAACGGCGAGTGTGTGTGCGGGACCTGCGAATGCAAGAAGCGGGAGAATCCAGAGGAGCGATACAGCGGGAAATACTGCGAGTGCGACAACTTCAACTGCGACCGCTCCAACAACAAACTCTGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:11
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=PD(9.5=60.3)
A:
NA
C2:
PF079748=EGF_2=WD(100=46.9),PF079748=EGF_2=PU(32.3=12.3)
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:
GCTGCCCTAAACAAGGCAAGA
R:
ATCGCTCCTCTGGATTCTCCC
Band lengths:
345-1679
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]