GgaINT0095057 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:14004212-14006080:+
Coord C1 exon
chr2:14004212-14004450
Coord A exon
chr2:14004451-14005857
Coord C2 exon
chr2:14005858-14006080
Length
1407 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
AATATCTTTTCAACGCACAGGAA
3' ss Score
5.79
Exon sequences
Seq C1 exon
ATGTAATGAAGGACGTATCGGAAGACTTTGTGAATGTAGTACAGATGAAGTAAATAGTGAGGATATGGATGCTTACTGCAGAAGGGAGAACAGTACAGAAATATGCAGCAACAATGGAGAGTGCATTTGCGGACAGTGCGTATGCAAGAAAAGAGAAAACACCAACGAAGTGTATTCTGGCAAATATTGTGAATGTGATAACTTCAACTGCGATCGATCAAACGGTTTGATTTGTGGAG
Seq A exon
GTGAGAAATTACTTCAGACTTCTCTGTAAGAAAACTGGCCAATAGTTTACAAATCTGTCAACCGTAGCCTGTAAAGTAGTTGTACTTAGCTTAAAAATACATAGCTATGTGATAACAGAGGTAATATGCAGAGTTTCAGAGGTTGAAAACATCTGTCTATTAATAAAACAGCTCTTTGCAGTCATGAGCATAGAGTGTTTTTACACATTTCATCTTCCTTGAATCACAGCTCCAAGAAGGATGTAACCTGAATTTGACTTCTGCTGTTTATTACAGAATTATCCTCAGATACTATAGTAAAGAATGCTGAGACAACTGTCCCAACATTATAAAGTTCTACTGGGTCAGTGTAACCACTGTGTCAATAGAAAGAGGTAGTGACCCCAGCTTATTTGTAATAGTGTTTGATTTGGTGCTTGACAAGATACCAGTGAGATGCTATCTTGAGACTATTCTGAAAGGTGAGTGAAGCTTAGAATGTGCAAGACCCAGGGAGACTCCTTAAGTGCTTGAAACAAGACTCTACATGGCAGTTAATTCTGAGATCAAAAGCAATTTAGAAAATCCTTTAGCACCTAAGGTCTGAGTTAATACTGATGCACATATTTTTGTCCTTTAACTTCCTTAGGCTCCTTTATATGTGGAAGTATGCAACGGGTATATAACCACTACTTCAGTTTTGACTGTGATCCAAAAATAAAAGAAAGAAGCCACTAAACTTTAACTGAATTAAGAGAATACCTATTCTGCCTGATTTATTCAGAATACGCCTGTTGTTCATCAGCTGTCCAAAGGATAGGAGCGATGGTGGTGTTGTCCTGAGACATGTGGTGACAGATGAGCATTGAGCTAAATGCTTTATTTTCCGTGGAGATGGAGAGATGTAGGGATAGATCTTTCCATCCAAACTGCCCCGTTGGGGATGCAAGTTGTAGCACCTGAATGAGGTGCTAGGGAGCCAAAGGTCTTCCGTTTTTCTTTGATATGAAGTCTAAGATCTTTTTAGATCTTACTTTATACAATTATGTAAAGATAGGTTCAGAGACAGTAGAGAAGTGCATCTACAAAATTTTCAGCTGAAGCAATACTGTGATGCTCTCTGCCCATGAAGTATTGCCATCACATTACGCTGTTCTTGATCAGCTGTCCCAAATCTTATTTCATTTATGAAAGGAAATCCAAATGTAGGAAGCTGGGAAAAGGAGAGAAACCTGTGTGGGTAGAGTTTCTTTCAAGTAATTAAAACTTAATCCGTAGCTCTTTTGCTTCATTAGTGCCATCCTTTTTTGGCCACCGGGGTTCTTTTATCCCTGTGTCTATCCTAAGGTGGCAAACATTTGTTTCTTACCGTCATAAATGTGTTTAATGTTAGACTTCATTTCACTGAAATATCTTTTCAACGCACAG
Seq C2 exon
GAAATGGTATCTGCAAATGCAGAGTGTGTGAGTGTTTCCCCAACTTCACCGGCAGTGCTTGCGATTGTTCTTTGGATACCACTCCATGCATGGCAGGGAACGGACAGATATGCAACGGAAGAGGAACTTGTGAATGTGGCACTTGTAATTGCACAGATCCCAAATTCCAAGGCCCCACATGTGAGATGTGTCAGACTTGCCTTGGTGTCTGTGCAGAGCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:12
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:
PF079748=EGF_2=WD(100=46.9),PF079748=EGF_2=PU(32.3=12.3)
A:
NA
C2:
PF079748=EGF_2=PD(64.5=26.7),PF079748=EGF_2=WD(100=42.7),PF079657=Integrin_B_tail=PU(4.5=5.3)
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:
GCAGCAACAATGGAGAGTGCA
R:
ACACCAAGGCAAGTCTGACAC
Band lengths:
343-1750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]