GgaINT0095059 @ galGal4
Intron Retention
Gene
ENSGALG00000007145 | ITGB1
Description
integrin beta-1 precursor [Source:RefSeq peptide;Acc:NP_001034343]
Coordinates
chr2:14007363-14009464:+
Coord C1 exon
chr2:14007363-14007595
Coord A exon
chr2:14007596-14009297
Coord C2 exon
chr2:14009298-14009464
Length
1702 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
TCTCTTGTTCTGTACCCTAGAAT
3' ss Score
9.09
Exon sequences
Seq C1 exon
GGACTGTGTTCAGTGCAGAGCTTTTGAGAAGGGAGAAAAAAAGGAAACGTGTTCTCAGGAATGCATGCATTTTAACATGACACGGGTAGAAAGTCGAGACAAATTGCCACAGCCCGGCCAGCCCGATCCGCTGTCTCACTGCAAAGAAAAGGACGTTGATGACTGCTGGTTCTACTTCACATACTCTGTCAATTCCAATGGTGAAGCCAGTGTCCATGTGGTAGAGACTCCAG
Seq A exon
GTATGAAACCTAATGCTGCCTTCTCTTCCTTCACCTTAATTCTCACAGATGCTGTATACTACAAAGTAGCACTGTTTGTTTTGCTTGAGTTGCATTGAGAAACTGTATCTGTTCCCTGTGTGAGAGATGCGGATATCCAGAACCCAAGTGGCATTTTAAAAATCTAAGTCTCTCTAGATCTGTTTTTTCTAAGCTTTAGGCTGACAGATACAAGTTTGGGGTTTTGTTTGTTTTTTAAAGTCAGTGAGATATGTAAGTTTGTTTTTCGTGTGTTTCATATTTCTGTTTGGTACCTCTGGGCTTGTATTACCTGTCCTGGAGCAACTTGTAAATACCTGAACTTTGCTTTCTGTTTTTTGACTGAGCTTATAGTGCACGTTAGAAGTAGTAGTGCATGTGGATTTTTGTTGCCCTTTTTGATTTTTAACAAAAGGGAACCAGTCTTGGACCCAAAGGGGGAAAAAAAAAACACTCAGCTTTTTATAAGCCTTACACAAAATATAAGCCTTATTTGTGTGTTGATACGCTTAGAACTCCTCAAGGAATTTTTGGATCTGATCACTTGGATGATCATCTCTTAATACCCATCAGTGGTTAAATTCTTCTCTGAGTTAAATAGCACTTCTAATTAAGAATGTTTTAAATTCTCTAGAAATGTATTCTAAAGCACTGAGCCCCATGTTCTCTTAGAACAAGTCAACACACGCCCAGTATGTATGGAACCTGGCCTTTTCTTCCCAGATAAATTTATGTTGCCATAGACAAGAGTGGAACCAAGCCATCTTGCAGCAGCAGGAGGAACCATGATGTTGTATGATGTGTGGGCACTAGAGGAACAAGCTCTGTCTGGCAGAGCTGGGTTTGGTGGAGCAGATGTTCATCCCTTACTCATTCCCAAAGAGTCCCTGCCCTATCTCTTCTCACTTCTCTCACCCTACAGTGTCATCTACCAAGACTAGGATTAGGAGTCCACAGTTTGTGTGGAATCACTGTTCATGTGGACATAGGGGTAACAGGAGTTCTCTTTGCTTGTGATACCTTCAGTCAGTGCCTTGAACTCTACAGAAGCCCTTCATCAGTTTGTGACTATTGAGAATTTTTCTTTAACTGGGTTAATTTTGAGGTTATTTTTGCCCATTAGTTAATGTAACACATTTTTTAACTGTGTTATTATTTTCAAACATACATTTACTTTGAAAGTGCTTAATATTTTCATCCAAAAATGTGACTTTATCTTCGGCAGAGATCAATTCCCAAAATGAGAAAATATCCTAAAAAAAACTGTCCCATAGAAGTAAAGTGTTAATTGCTAAATATATAGAAATAAGTAATAGAACTAATCTGGGATAAAAAAGAGGATCACCATTTCCTTATAATGCTATCTATAGAGGCTGTTGACTGACAAACTAGACATTTGTCCCTCTAGCACCATCTTTGATTCAGAGCTCCTGCATGTTTAAAATACAACCGGTAGTTATTTGATCCAAATACTCTAAATGAACTAAAAATTAGAAGGAAAAAACGTGGAACGTCCCAAAGATGTACCGTTCCAAACTTCTGTAATTTGACATGAAAGTAGTGTTAGCATTTCTCAGATATTTGAAGTAATGGCTTCAGTACAAACTGAACATTTTAAAAGCATCTGAATAGTCATTACCTTTTCCATTTTGTAAAGTCATGTTTCTCTTGTTCTGTACCCTAG
Seq C2 exon
AATGCCCTAGTGGCCCTGACATCATACCCATTGTAGCTGGCGTGGTTGCTGGAATTGTTCTTATTGGACTTGCATTGTTATTGATTTGGAAACTACTGATGATCATTCATGACAGGAGAGAATTTGCTAAATTTGAAAAGGAGAAGATGAATGCCAAGTGGGATACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000007145:ENSGALT00000011573:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.101 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=FE(87.6=100)
A:
NA
C2:
PF079657=Integrin_B_tail=PD(6.7=10.7),PF087256=Integrin_b_cyt=PU(53.2=44.6)
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:
CGTGTTCTCAGGAATGCATGC
R:
CGTATCCCACTTGGCATTCATCT
Band lengths:
353-2055
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]