GgaINT0095049 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:13994969-13997284:+
Coord C1 exon
chr2:13994969-13995191
Coord A exon
chr2:13995192-13997113
Coord C2 exon
chr2:13997114-13997284
Length
1922 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
TTGTTTAATCCGTGAAACAGGGG
3' ss Score
4.44
Exon sequences
Seq C1 exon
GACTTTCTGCAAGAAGGAGAACCAACATCTGCCCGATGCGATGACTTGGCAGCGCTGAAGAGTAAAGGCTGTCCTGAGCAAGATATAGAAAATCCCAGAGGTAGCAAACGTGTGCTTGAAGATAGAGAAGTAACAAATCGTAAGATAGGTGCTGCAGAGAAGCTGAAACCAGAGGCCATTACACAGATCCAGCCACAAAAATTAGTACTGCAACTAAGAGTCG
Seq A exon
GTAAGGATGGTTTCATTCCAGTTTTTACTTGATTTTCCTGCCACCACAACTGCATTTTGTGTATTAAATGTATAATCATTTTGTTTCAGAAATGATTATTGTTCAGATAATGTGAGTAATAGCAGAACTATTCAGGTTAACCCCAGGTGTTGAGGTACTTCGAATGCTGACAGATTTGTATAAAAGATAAGATAGTTTTTTATCTCGTGTTCTCAATATATCTTCTGAGAAAACCGATACAGATCATAAATATGTCTGTGTGGTTCAGCAGATGTATCGAAAAGATTAGATTCTTTTGTTTTCAGTAATATGCAGTTCATTTTCTGCAGTGCCACTTCTTGGAATGGCCGTGAAGGAGTGTGCAAAAACCTGTTAGGAGAGCACATCCTATTCCTTGAAGTATTCCTGTTGTCCGAAGTCTGCGTGACTGAGCAGAATGGTTTTGCAGTATGCAACAAGATTATCAGTTTGCTATATAAGATAGGTTCCAGGAGTTAAAGAAATGGATACAGAACTGAATTAATGAAAACAGAGCAGTTATGTACCATTTCAAACCCATAAAGAGAGATTTTATTCAGATGGATAGCAGGAAACAAGTCCTGTAGTTCACACAGTGCTTGAACACAGAAGGGACTGTTCTTAAGAAGAGTTCCTAGGTGCTGTAATCCTACGTCCTAAAAATACCTTGCATTTACCTGGGAGAAGAGCCTATACATGGAGCTAGCTGCTTGTAGGGGGCTGCCGTAATAAGTGCAAGATGCTCTGAGGCAGCTTAGCATAACGAGAAGGAAAGAAAAGGAAGGAACAAAAGTCCTTTTGCAGTTTTGGAGTTATCTCTGTTTAGTTCTAGTTACCCTTTCGGCTTCAAGAGGCTAAATAATCATCACCCTATTGACAGTGTTCAGCAGACACATGAGGGACCTGGGCAACCAAAACCTAATGACCCAAAAGCTCAGCGCTCAGTTTACAGGCACTTCTCTTGGTCACAGGTTCTCTGATTAGAGACTGTGCATACAGAGGGGATGTTTGTTTTCTGTGCAGGCTCTTTTAAACAGTAGCTAGGGAAAACCCCAATTTTTTTGTTTGTTCTGTTGCTGCGTGGCTGCCAGATCCTTGCATTCATCTCCTTTACCCACCCTATTTTCCTAATATTAAGCAAATATTTGCTAACTATTGAGCAGACTTAATCAGCAGCAGAATCCCTATTTAACTTTAGTGACTAAAGGATGGGGTGGAAAAAAAGACTTCTAATTCCATTCCTTATTTCATATACAATAGGCAAGAGAATTCTTTTCCATTTAACTTGAGGGCAATTCTGCACTGTCTTCCAGCATCAGAGCAGGACATGTGCTTCTGTTGGCAAAGCTCAGGGCCTGGGCTTCCAATTGCAACAGACAGTAATGGATTGTCTCACTGCTACTTCTACATTCTCAGTCTATACTCAGTGCGGAGTAACTTTAAATATTCTACCCAGAACTGTTGTATTTTTTATAAACCTATTTTAACACTGTTATTCCTAAACTAAACCCTTAGAATTCCTGCAGTCATCTTGGATGCAAATAGATATGGAAAATTGGTGTTATTAGACCTTACAGGAGCCTTGTTAAAATTATGGCAAGCATCAAGATTTAAAACTGCAGTAAGTAAGAAAGGCTCGATTTGTGGCAGGCTGGTATCTTCTGTGGGGAGATAGAATGCCTTAGCTGTGTGGTGCTGGGCATCTGAAAGAAATGCTCTGTGAGGTTTTTTTCATTGTAATTCAGTGTTAATCGTATCAATTAACAGAAGAAAAAATCACCATTAATTAGTTCAAAACCTCCATCAATATCTGTAAGGCTTGACTTTAAAAGGCGTTTTTTCTGCTGTTGTGCTTCTTGTGGAATTTGTAATGGCTTCTGTTTGTTGTTTAATCCGTGAAACAG
Seq C2 exon
GGGAACCGCAAACATTTTCATTAAAATTTAAGAGAGCTGAAGATTACCCCATTGACCTTTATTATCTTATGGACCTCTCCTATTCTATGAAAGATGATTTAGAGAATGTGAAAAGCCTTGGCACAGCTCTGATGCGTGAAATGGAAAAAATAACCTCAGATTTTCGAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.156 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(17.1=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(13.2=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:
GAGAACCAACATCTGCCCGAT
R:
TTTCACGCATCAGAGCTGTGC
Band lengths:
348-2270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]