RnoINT0076302 @ rn6
Intron Retention
Gene
ENSRNOG00000010966 | Itgb1
Description
integrin subunit beta 1 [Source:RGD Symbol;Acc:2927]
Coordinates
chr19:61712642-61714640:+
Coord C1 exon
chr19:61712642-61712841
Coord A exon
chr19:61712842-61714401
Coord C2 exon
chr19:61714402-61714640
Length
1560 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
GTGTTTGGATTTCTCTGCAGGTG
3' ss Score
11.07
Exon sequences
Seq C1 exon
GTTCAATTTGAAATTAGCATAACTGCTAATAAATGTCCAAACAAGGAGTCTGAAACAATTAAAATTAAACCTCTGGGCTTCACAGAAGAAGTAGAGGTGGTCCTTCAGTTCATCTGTAAGTGTAATTGTCAAAGCCATGGCATCCCAGCAAGTCCCAAGTGCCATGAGGGAAATGGGACATTTGAGTGTGGAGCCTGCAG
Seq A exon
GTAAGTGCAGTCTTGCTGCAGTGGGACAGACAGTATAGGCCACTTTATTTGGGAAGCCTGTAGAAAATAAAGACACGAATCCTTTGCTTCAGTCACTTGCTCACCTACTCTTAAGGCTCTGTGGTTAAGCTTTTGCTAGGTAAGCAGTGTGTCCACTCAGTGTCTCACAGCAACCTGTGGGCTTTGTTCTCCTAGTGACACTCCCAGTTCTCTACAGTAAAATACATTGAAAAGGGAAAACAAGTAGACAGAAACATGTTTTGCACAGACTGTCAATGGTGACTTTTTAAATTGTGTTTTACTTGGATGACCCCAAATTTATGATCTTACTGCCTCCGTACTTGGGTACTGAGATCCCACTCCTCCCAGTCTTAAATCACAGTTTTATCTGTGACCTAGTTAGCAAGAAAAATGTTTACCATGTACAGCATTAATTTTCTGTTTCTGGGATAAAGATAAAATAGTACTTGAAGTTTCATTTATTTGTTTATTTAGTGTGTGCTCTGATGTTAGGGCAGGCTTGTGGTGAGAGCAATCACAGAGTTAGTTCTCTGTTTACCTTGTGGATCCTAGGAGTTGATCAGGTTTGGTGACTCTTTTTTTGGTGCTTTTAGCATCTTAGCCGTCTCACCTGCCCTCTTGGCTGCTTTTTATATTAAAAATTAAACTGTGTTTGTAATACAGCCTTTTCTTTAAAATAGAATTTTTTGTAAATGTCAGCCTCATATCACTGTGGGTTTTTTTATTGGCCCAAAGAAAAATGAATAGCTATGTTTACCATTAATTGCCATTTTAAGAAATGATTTAATTATTGTATTCTTTCTACATTATATTTAACTTGAGTCATTAAGATATCTTTTTTTTTTTTAAACAGCATTTACCAAAAAAGATCTTTTTTGGAATTTCTTTGCCTTCTTTTTGTTTAGCATATGCAAAATGAGTTTATCCAGTATTCATGAACGTGCTCTAAGATATGTAGGATATTTGAGCAGTCTAGACCTGTGTGTAAATTTACCCTTATCTAAGGCTAGGTCTATTTTCAGTTTATGTACTCAGTGAATTTTCTAACTTTTGGGATTGTAGGCATTGCTATTTTTTTGTTAACAGTTAGACCTTTGCTTCAAATTTAGTGGCAGGTAGTCTGTAACGGTAATATAATTGAATTATTTGAGAATGTAGCCAGATGTACACCTTTAATCCCTGCACTTGGGAGCTAGAGGCAGGCAGACCTCTGAGTTCCAAGTTAGCCTGGTCTGTTTCTTCCAGTTTTGTTGTTTGTTGCTGGAGTATGTTTTCATTTTGCTCAGAATGGTTCCTTGCTGAAGATGAAATTTCCCCAAGGCCCCTGTATATTCTATAAGAACTTGAGTGTCTCCTGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGAACACAGTGCACTTCTCTCAGGTCTGTATATGTAGAGCGAGCATCCCTCCCTGATACTTTGCTAGTGTGAGGAAATTGTTGCACTTCGTGTTTTATGTGACTGTGTTTGGATTTCTCTGCAG
Seq C2 exon
GTGCAATGAGGGTCGTGTTGGGAGACACTGTGAATGTAGCACAGATGAAGTGAACAGTGAAGACATGGATGCTTACTGCAGAAAAGAGAACAGCTCAGAGATCTGCAGTAACAATGGAGAGTGTGTCTGTGGACAGTGTGTGTGCAGGAAGAGAGAGAATACAAATGAAATTTACTCCGGCAAATTCTGCGAGTGTGATAACTTCAACTGCGATAGGTCCAACGGCTTAATCTGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010966:ENSRNOT00000014785:11
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:
PF0036213=Integrin_beta=PD(9.3=59.7)
A:
NA
C2:
PF079748=EGF_2=WD(100=46.9),PF079748=EGF_2=PU(32.3=12.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCTGGGCTTCACAGAAGA
R:
CCGTTGGACCTATCGCAGTTG
Band lengths:
357-1917
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]