GgaINT0095058 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:14005858-14007595:+
Coord C1 exon
chr2:14005858-14006080
Coord A exon
chr2:14006081-14007362
Coord C2 exon
chr2:14007363-14007595
Length
1282 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CTGATTATGTATTTCCACAGGGA
3' ss Score
9.18
Exon sequences
Seq C1 exon
GAAATGGTATCTGCAAATGCAGAGTGTGTGAGTGTTTCCCCAACTTCACCGGCAGTGCTTGCGATTGTTCTTTGGATACCACTCCATGCATGGCAGGGAACGGACAGATATGCAACGGAAGAGGAACTTGTGAATGTGGCACTTGTAATTGCACAGATCCCAAATTCCAAGGCCCCACATGTGAGATGTGTCAGACTTGCCTTGGTGTCTGTGCAGAGCACAA
Seq A exon
GTAAGTAACTAGAGAGCCAAATCCCAGCTTATGTTTGTTTGGCTTTGTGATACATGCTTATGCTGAATATTGAAAATGAGGCTTTTGATACTGTGCTCTCTCCTATCCTGAAATGTAGGAATATCATGTAATCCCTTTAGATAAACCAAGTTGTTGGATGAGCATCAAGAAATACGGAATAAACAGTATTTTGATTGCTCCCAGATAGGCTATTTATCTCTTAAATTATTTCCCTGCTGGTTTTTTTTTTGTTGTTGTTGTTATGCACAGAAAAGTGTGTGTTGTTAAATCAGTTTTATCCATTCAGATTGATTTGACTGACTTGGACAGGTTACAGCTTTCGTGTATGGGTCCTAACAACCAACATTCTGCAGAGCTGAAGAAAGCATAGGCCGTAGTGCAGCAGGCCGGGAAGTCCCATCTTGGCCTTTTGAAGTTCACATAGCAAAAATAAGCACAAGTACACTGCTGTCTCCAGAGCAGTTAAAATTTCAGCTAAGCTCTTTCTTAAGACTTCTGTTTTATTTTAAGTCGTTTAAAAAAAAAAACAACAACAACTTATTGAAAGAATGCTGTTGTGCTGTTATAATTTAATAGATTATTGAATTATTGATTATTCTTGATAGCCAAAAACTAAACCTTGATCTGTGAGAGCCAATGAGATTTGCATCCCTGTGTTAGGAAATCCAGGTTTTTGGAAGAGAAGGATTTTCTGCATGCAAAGTTTTGAACTAAGTTTGTGATTGGTGGCTGTGCTGACTCCTGGCATTAAGGATTCTCTCAGCTGCTATAAAACTCCTGATGAGTCTGCTTTTTTTCAGTGATGTATTCAGAGTGATAACTTATCATAAAGCTCCTCACCCAGTTTGTCCTTTATAATCCAGTAGCTCAGATAGTGTTCTATTGCAAACCTTCTGTTCCTGCTCTAGCTTGTCTGAGAGTATTCGTTCTCCTGGTGGAAATGTTGGAAAAAGTTTTAGGTATCATTCCTTTTAGACATTTAGTTCCTTTAGGCTGGTTGGTTGGTTTTTTCCCCTCCCTATCCTTGAAGCTCGTGAGTCATATTGTTAAAGAGGAATTTGGTACAGCAGGTCTTTGTTAATCTAAAGGTATATCAATGTTCTGACTGGTAAAAAGTCATGTCTTTATTTTTTTTCTGGTTTTAATATCAATGTTTGTTTGTTTGTTTTTCTTTTTCTCCTTTACATTTCCTTACATTAAATGCTAGAAAGCTTTTGTGAACATTTGAGAAAGCATTGTTTCTGATTATGTATTTCCACAG
Seq C2 exon
GGACTGTGTTCAGTGCAGAGCTTTTGAGAAGGGAGAAAAAAAGGAAACGTGTTCTCAGGAATGCATGCATTTTAACATGACACGGGTAGAAAGTCGAGACAAATTGCCACAGCCCGGCCAGCCCGATCCGCTGTCTCACTGCAAAGAAAAGGACGTTGATGACTGCTGGTTCTACTTCACATACTCTGTCAATTCCAATGGTGAAGCCAGTGTCCATGTGGTAGAGACTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:13
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=0.101
Domain overlap (PFAM):
C1:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
A:
NA
C2:
PF079657=Integrin_B_tail=FE(87.6=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:
TGGCAGGGAACGGACAGATAT
R:
TCTACCACATGGACACTGGCT
Band lengths:
358-1640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]