GgaINT0095056 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:14002215-14004450:+
Coord C1 exon
chr2:14002215-14002417
Coord A exon
chr2:14002418-14004211
Coord C2 exon
chr2:14004212-14004450
Length
1794 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAT
5' ss Score
7.25
3' ss Seq
GTCATGTTCTTACCTTGCAGATG
3' ss Score
11.58
Exon sequences
Seq C1 exon
GTTAGGTTTGAGATTAACGTAACAGCAAATGAATGTCCAAAGAAAGGGCAAAATGAAACAATTAAAATTAAACCACTGGGGTTCACTGAAGAAGTGGAAATTCATCTCCAGTTCATCTGTGACTGTCTGTGTCAAAGCGAAGGAGAACCTAACAGCCCTGCCTGCCACGACGGAAATGGGACATTTGAATGTGGTGCATGCAG
Seq A exon
GTAGATAAACAGACAGCTTACTTATCTTTGCAAAAGGGAAATATGAGCTATACCTTTGTTTCCTTAACTGAAGTTTATTTGAGTTTAATAGTTTTTGAGTGAAAGAACAAGAATTATTGTTACAATCCTGTTTCCTGTGGGGCATTTTGACATATCTCATATCTGCAAATACTCTGTGCTAGAAGTCATAGTGTTAGATTGATACTGTTGTACAAGTCAGAATTAGAATTCGGCCTTTATTTAATCCCTTAAATCCCTTAGCTGATATAGGGCTTAATGCTTTTTTTTTATTTCCCACATTTAATTTTACAAGTGTATTTATGGTAGAGAAAATTAATGATTACTTTGTGATATTTTTGCAAATACTCATACTGGTTTAATTTTATCTTTCTAATGTAAAGTCTACTGATTTCAAGAAGTTCAGAGACTTTGTAGTTTGTGATAGGAGCTCCTACCCAGATTGGCACCAATTGCTTCAAAGAAGGGAGAAGTGAAAAGAGCAGCCTTTTATTTTATTACTTATCCCCCCCTTGCTCTCTTTTCCATGCTTTACTTGGAACTTTTGGGGGCCTTATTACAGTATTTTTTCCAACTGCATACATCTGTAAATCTTTAGGAATTCATATAATCATTTGTCTAACTATGCTTTTGGAACTTCCATTATTTCCCATTATACTGAATTTTCTGGAGTTAAATGCCAGCTGGAGAGCAGTTGAATATCTACTTAATAAGTCGGGGTTTAAGCCATTTTTTCCCAAGAAACAGACAGCAAAAATGAAAAGCATTTCTCGTTGGAAACCCTTGAGACATGAATGGTAAGAGCTGAATGCAATTAAGTACTTCCCTAGGAAAACAGGATCCAGGACTTCAGGGAGCTGCACTGGACGGTTCCTGCTCAGTAAACTGCATCTATAAATAAATAAAAATATAAAAACGAAAGTTACAAATCTTGTTCTTAAAACTTTGTGACTATTTATAAAAAATAAGGAAAAAGTTATTGACTTCTAGCTTATGGGACTTTGAGTATAGAACAGTCTTCCTGGTGAGGCTGATGACAGTAGCTTGAATGCTTGAAAGACTGAGGTATGACTAATTCCTGAGTATTAAGTAAGCTGAGGAATAAGCTATTTCAGACCATATGCAGTAGATAAACTGCTTAATTTTGCAGTTATTTTTTATGTTCTCTTTAAATAATGTAAGCAGCTTCTCCCATCGTTGTCCATAGAAGGAGTTATTAAACTTAGCATCACTGTCACTATGTGTCTCCGTGGTTTGTTGCAAGGGTAAAACCTCCAGGTAAGAACAGCATTTTGCTTTTGCAACAGGAGCAGTTTTGTGATGGAAGCATTTTCTCTGATTGTCTTTTTGACAGCAGCTTGTCAATAGCTGAACAAGAATAACCTCCATTTACTCATCAGTGTTTTTGCCTTGACGATGGGAAGGCTGAATCCCAATGGTCCCAGTTGAATTTGCTGGTGCTCAGCAGCTCTAAAGATCAGCTGCTCCCCTGCCTAATTGCTGTTCTTGGGAGAATTCTTTCACTGAAAGTTGACAGCACCTACATTGAGCAGTTATTGTCACTTAAAAGTAGTTATGGTTCTGTCACTGTAGAGAGGAATTAATAGCGGTTATGTGGCAATCTAGCTAGGGGTGTTGACACTTTTTCTCACCTGGAAAACGTTGTCAATATAAGACCACCTTCATCCAGCTAAATCCAGCAGCTTCAAGAGCTGTTTTATTTGCCCAGAGAGGTTGTAGATTTTCACATTTTTCAGTCATGTTCTTACCTTGCAG
Seq C2 exon
ATGTAATGAAGGACGTATCGGAAGACTTTGTGAATGTAGTACAGATGAAGTAAATAGTGAGGATATGGATGCTTACTGCAGAAGGGAGAACAGTACAGAAATATGCAGCAACAATGGAGAGTGCATTTGCGGACAGTGCGTATGCAAGAAAAGAGAAAACACCAACGAAGTGTATTCTGGCAAATATTGTGAATGTGATAACTTCAACTGCGATCGATCAAACGGTTTGATTTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:11
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACTGGGGTTCACTGAAGAA
R:
ACCGTTTGATCGATCGCAGTT
Band lengths:
357-2151
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]