GgaINT0095052 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:13998682-14000088:+
Coord C1 exon
chr2:13998682-13998837
Coord A exon
chr2:13998838-13999992
Coord C2 exon
chr2:13999993-14000088
Length
1155 bp
Sequences
Splice sites
5' ss Seq
TACGTAAGT
5' ss Score
9.27
3' ss Seq
ATTTATTTTAATTTAAACAGGAT
3' ss Score
7.6
Exon sequences
Seq C1 exon
GACCAGATTGGATGGAGAAATGTTACACGGCTGTTGGTGTTTTCCACGGATGCTGGATTTCACTTTGCAGGAGATGGTAAACTTGGTGGAATTGTTTTACCAAATGATGGGAAATGTCACCTGGAAAATAATATGTACACAATGAGCCACTATTAC
Seq A exon
GTAAGTCTTTACTTTGTCTTTAACTTTGTCTTTTACTTTGTCTTTAATTAAATCAATTAAGTCAACTGGCATATTTTCTGAACGCTACATCTTTTGAAATGTACCCTTTTGCCTCTATATTAAATCAAGTGACTTCTGCATGAGAAAGGCAAAACTGCAAGAGTTGATGTTGTCATGGTTGGAAAACTTCGGGAAATGTCAACTTTCATTTGTGGTGGTTAATAACTCTGCTCATCCACTGGCAAACTGTGCTGCTGGCTCTGTCCTGTTATTTCATTCTTTCACTGTTATTTGTGTTTAGAAGTATTTCTACTACTGCCCAGTTATACGTAGCGTCATACTTAGCTTCTTTGGGACCCAGATGATAGAATCACCTGTAATTAGTCTCTGTTCATGAGGGTTGGCTTTTTTATTTGATTTTATTTCATTTTTAAGTCTGGAAGGCATTTTGAGTCGTTTGAGCATGAGCTCTCACTGACTGAGTATGCTGCTCATAATTATGCACTAATTGCTAATTGAAATTCTGTAGAATCCTAAGACTGCTTGAAATCTCACAATGCCGAATTTATGGTAAGTAGGTTAGCAGCATGGCCACTCTGGTTTATTTGAGAGGTGGAGTAGAGGAAAGGTGAAAAGAAAAACATTTACTGAATAGGGTAAGCACAGTAAGCCTTACCAAGTTTGCACGTTTATATATTCCTAAATTTGAGTGTTTCTTCGGTGACAACTTAAAATTTATTCAGTTTTATTTAATATTTTCTTTTTGAAATAGTACCAGAAGTGGTTTTCATGGTATGAAGTCAAATACCTTTTCACAAATGTATGGAAAAATATTGAAGGTAACTTTGTGAGAATATTGAAATTAGGAACTGGAGGATTTCAGCGTCAGGCAATATGACAGCATTTCTGTTGTCCCTTCCAAAATCAGCTCTCTCCCTGGGGCATATATGGAATCTTTTCAATGGATATTGGTTTGCAGGGGTGGCTTTGATTTGGAGCTGTAAGATAAGCTGGCTAGTTGGAAGTCTGACGAATGCTTCTAAAATTATTTTGTATTTATAACATCAATATGTTGATTATTTTCTACTATGTAATCATAACTTTGTATCATAACTTTGGTTTGCTTTATTTATTTATTTATTTTAATTTAAACAG
Seq C2 exon
GATTATCCCTCTATTGCTCATCTGGTACAGAAGCTTAGTGAGAACAATATTCAGACAATTTTTGCTGTTACTGAGGAGTTTCAGGCAGTTTATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:7
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCAGATTGGATGGAGAAATGT
R:
AACTGCCTGAAACTCCTCAGT
Band lengths:
246-1401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]