RnoINT0076304 @ rn6
Intron Retention
Gene
ENSRNOG00000010966 | Itgb1
Description
integrin subunit beta 1 [Source:RGD Symbol;Acc:2927]
Coordinates
chr19:61714845-61716959:+
Coord C1 exon
chr19:61714845-61715067
Coord A exon
chr19:61715068-61716726
Coord C2 exon
chr19:61716727-61716959
Length
1659 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TGTAATGATTTCTGTCTTAGAGA
3' ss Score
7.11
Exon sequences
Seq C1 exon
GAAATGGTGTGTGCAGGTGTCGTGTCTGTGAATGCTATCCCAACTACACTGGCAGTGCATGTGACTGTTCCTTGGACACTGTTCCATGCGTAGCGACAAATGGTCAGATCTGCAATGGCCGGGGCATCTGTGAATGTGGTGCTTGTAAGTGCACAGATCCCAAGTTCCAAGGGCCAACCTGTGAGACCTGTCAGACCTGCCTTGGTGTCTGTGCAGAGCATAA
Seq A exon
GTAAGTACTGCCCAAGGGCTTCACGCGGTCACACTCACTTTGCTGACCCCAGTGCCTATGTTACACCACTAGAGCCAGAGGAGAGTGCTGATCGAGTGCACTTCTAAGAGAATACTGGCTGCTTTTTATGTACCATTTTTTATGTCCTAAAAATTCTTAATAATTGTGTAGGAATGAAGTGTGCCATGAGAGTTGTGCTGTTTTGTTTGTTTTTAATCTGAAATCACTATGTAATAAGTCTGTGCTGTTACCTTATTTAATCGGCACTACTGTCCTTTGTTTTTAAGGTTTAGTGTAGAGATAGAGCTCTGAGCTCTACCACAGAGGCTTATACTCTAGTCCAGTTGCTATCTTTTGCTTGAGGAGAATGGAAGGTTTTCTCCTTGGTAAATTATTATACTGATACTATACTGCTTAAGATATTATGGATCTATGTTACATATTTGATGTCATATAGGTCCAGTTTTATTACCTATATCTTAATTTTGTGTTGTAGAGATGTATATCCATGCATGTGTATATTTATGTATATCCATGAATGTATATATATTATGTAAAGTTATGACAACTTTAGTTATTTCTCAGGTGCCTTCTACCCTGCCACCTCTATTTACCAGAGGGGTTTTCATTGACCTGGAACTTTGCCAAGTAAGCTAGGCCAGGAATCTGTCTCTGCCTCCTAGCACTGGGATTGAAAACACGTGCCTCCATTACTGGCCTTTTCCATAGGTTCTAGTGATCAGAATTCAGGTCTTCATGCTTGTGGGGCAGGTACTTTTCTGACTAAACAATCTTCCAGGCCCCACCTTTATTTCTTTATCATGATTTAATTTTCATTTTGGAGACTAGCATTTTCTTTTTACCCTATTAATGAGAAATTTATTTGTAAGAAAAATCCAAGTGTTAGCATTGACTAAGAAAATGTATTTGGTTTACTTAAAATTGCTATAAATTTGAACTGCTAAAGTTCATTAAAATATGTTAAATTATGTTAATTTTATATATCTATATAAATTCATACACAGTGTAGAATGAGAGAGAGACCTTGCTATTGAGCCTAGGCTCTCCCAGAACTGGAGATTATTCTGCCTCAGCCTCCTGAGCATGCTAGGACTGCAGATGTGGCTACCACTAAGGGCTTAGTCTAGATTTTAATGTATGTCCCCCAGGTCTGCAGTGTGCTAGTTGTTAGTTTGTACTGGAGGCTGAGCAGTTCCCCATAGCTAGGAAGTAAGGTTTGTTAATCAGATGTTGGGTGAACTCTTGATAAGGCCTGGTGTTACTAGGCCCCATAGGCACTGGCCTTTACTGAAGTCTTTATTCTTCCAGTGGAGGGCACATGCTTGCAGGCAGCTTCTGTAGCCAGAGGCTTCCTGGGTGCTTTGCTACAACCAATGGTTAGTCCAAGGTGGGTCTGGAGAATTTGTTACCTACCCTTTTATTCTTTGACTGCAGCTTTGCCAGCCAGGGTGTTGCTGACCTTAGTGGCAGTGGCTTGGCCAAGGCTGCTGGAAACCAGGATCTCTTGTGGCACATATTACCTCTATTTCCTCTGAATTTATATTGCCCTTAGACTGGTATGGTTATTAGTTTAGCACGTGAAGTATTCTAAGCAAAATTCATCTTAATACACACTAAGTGTAATGATTTCTGTCTTAG
Seq C2 exon
AGAATGTGTTCAGTGCAGAGCCTTCAATAAAGGAGAAAAAAAAGACACGTGTGCACAGGAGTGCTCCCATTTCAACCTCACTAAAGTGGAAAGCAGGGAGAAGTTGCCCCAGCCTGTGCAGGTGGACCCTGTGACCCACTGCAAGGAGAAGGACATTGATGACTGCTGGTTCTATTTCACCTACTCAGTGAACAGCAACGGTGAAGCTCACGTGCATGTTGTGGAGACTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010966:ENSRNOT00000014785:13
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=0.013
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
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGGACACTGTTCCATGCGT
R:
CACCGTTGCTGTTCACTGAGT
Band lengths:
356-2015
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]