GgaINT0095051 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:13997543-13998837:+
Coord C1 exon
chr2:13997543-13997781
Coord A exon
chr2:13997782-13998681
Coord C2 exon
chr2:13998682-13998837
Length
900 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGC
5' ss Score
7.79
3' ss Seq
TTGTTTTTTTTTTTCCTAAGGAC
3' ss Score
9.21
Exon sequences
Seq C1 exon
GATTTGGCTCTTTTGTGGAGAAAACTGTGATGCCATATATAAGTACAACACCAGCCAAACTGAGAAATCCTTGTACAGGTGACCAGAACTGTACGAGTCCGTTTAGCTATAAAAATGTGCTCAGTCTTACTAGTGAAGGAAATAAGTTCAATGAGCTTGTAGGTAAACAGCACATTTCTGGGAATCTGGATTCTCCTGAAGGTGGATTTGATGCAATAATGCAAGTTGCTGTTTGTGGG
Seq A exon
GTAAGCATGTACTGGTTTTCTTAAAGTGACATGTTCTAAATTGTTGCTCAGTTAGATGAAATGTAACAATAATACGGCCTCAGTGTTCATGGCGGCTGGCCTGATGTTTCAGTTTGTCCCACTTCTGATAGCAATATAAGGTACCCCAGGCAGACTGTATGAATACATGGACTTGTTTTGTGTAGGCATGCAGTGAATGGATGAAAGCAGCACATGTGAAGCATATGGTCACAGGTTGTGTTCACAGAAGATGAATGCATTCCAAAATTGATGTTTTTAAAGGTTTCTGTAAAAGAAAAGTCCAATTCTGCTCACGAGTGTATGGAGTTGTGAACTGGCAGTTATGCTCCAATTATTTCAGTCTTATATGCTGCTTCTAGCTCAGGTTTCAGAGCAGCTTGATGAGTGGTAATTTCTACCAGCTTCTTAGACAGAAGTAGATCAAAACAAGACTGTTGTATGTTTTCAGAGTTCATATCCAACTCACTGCTGCCTTTCACGTTTCTGATCTGACAGACAGTTCTATGTTCCTATGCTATACGAACTGCCCAAAAATGATATCCAAGGCTACTCTTTGTTGCTGTATTGTTACACTGATGATCAGTGGTGTCAGGACTTCCTGAAGCAATCCAGAGTCTTGTTTGAAAAGAGCAGAGAGAGTGTTCATTACCTTTGGTGAAAATCCTGCAGCAAATATTTTAGAGCACACGAATATAAGTGCTTATAATGTTTGAGTGAATTATGGAATTTCCAGGATGATGCCTTTATTGTGTGGCTTCTCCTAAGTTTATCAGGCACTCTCTGCTTTATCATGCACTTACCTCTTCAGTGTTGCTCCATATTGCTCAAAAAGAGTGGTACAAAATACTTAAACTGGTTGTTGTTTTTTTTTTTCCTAAG
Seq C2 exon
GACCAGATTGGATGGAGAAATGTTACACGGCTGTTGGTGTTTTCCACGGATGCTGGATTTCACTTTGCAGGAGATGGTAAACTTGGTGGAATTGTTTTACCAAATGATGGGAAATGTCACCTGGAAAATAATATGTACACAATGAGCCACTATTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(18.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(11.8=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:
TGTGGAGAAAACTGTGATGCCA
R:
TCCAGGTGACATTTCCCATCA
Band lengths:
351-1251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]