RnoINT0076311 @ rn6
Intron Retention
Gene
ENSRNOG00000010966 | Itgb1
Description
integrin subunit beta 1 [Source:RGD Symbol;Acc:2927]
Coordinates
chr19:61706487-61708799:+
Coord C1 exon
chr19:61706487-61706725
Coord A exon
chr19:61706726-61708643
Coord C2 exon
chr19:61708644-61708799
Length
1918 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
GTAACCTTTTTCTTTTACAGTCG
3' ss Score
9.77
Exon sequences
Seq C1 exon
GCTTTGGCTCATTTGTGGAGAAAACTGTGATGCCATACATTAGTACAACACCAGCAAAGCTAAGAAATCCTTGTACGAGTGAACAAAACTGTACCAGCCCATTTAGCTACAAAAACGTGCTTAGTCTTACTGACAGAGGAGAGTTTTTCAATGAACTTGTTGGTCAGCAGCGCATATCTGGAAACTTGGACTCTCCAGAAGGTGGCTTTGATGCAATCATGCAGGTTGCAGTTTGTGGG
Seq A exon
GTAAGTGCTTTCTACAGGACTGTTTGTTTATACCGTCTGGGGAGTTCTTCTGTGTGTGTTTTTACTAAAAGTTAGAAGAAAATAACCTTAGCTACTATAAGATTACCTGAAGAGCACTGATGTCCGCTCTTAAGTTTCCACCGCTGCTTTCTTGGGTATCTCTAATCATTGCATCTCTGTTTGAGCCAGAAAGGGAGTTCACACCCAAGGAGTGTGAAAGGCCAGTATGTGTTTATTTGAAACAATGGAACATAGACTTTAGCTGATTTAGGTTTTTGGAAGAGGCTGAGGTGTCCTAACTTTGTGGCTCTGTATTGGAGATGTAACTCATGTTTGAGATCTCTCCAGGAACTCTGAACATGCCATATATACGGTATAGTGTCTCACACCATGTTCCTCAGGTCAGTTTTCTGCTCTGGTCATTGCTTTGACACATGTATTCCTCTGGTGTCTTAATAATAAAAGGGAGGAACTTTCAAAGGCTCGATGGATGAGCTGTATGACAGCTTAGGTTTGTAATAATAGTAATAGAGTACTTTTGGTTTAATTGTAAGGTTTCAGGGGTAATAATAAGCCTGGTTCTGTTGAACCAGGGCCAGTGTTTATGATCCATGGGTATTTCTGATGTTTTTTGTTTTTTGGAGATATGGTTTTGCTGTGTGGCCCAGCAAACTTGTAGAGATGTTTTGCCTCTACTTCCTGAGTACTGGGATTCTGGGTATGGTCCACTACACCAGACCCTCAATGATCTTTTAATGAGAACTGTGACCCAAAGTAGAAAACAATGTTAGGTCAATAAAGCTAGTCTAGAGTACCTTACTGTGTAGATCTACTTTCCACTGTAGATATCCCAGATTAGTAAGTATAAAGCACAGTTTTAGTATGGAGAGGACTTTTCCTGTCCTTGCTCCTAAGGCAGTTGACTTTGGTATCTTTAGAGCTGTGCTTTTTGTAAAAGTTAATGACAGCCCACGGGACAGTTGTAAGGACCATCACAGTGTTCTGTATGAAGTACACATAGACACTCAGCATATATTGAGCACTGTTTTTATTTTTGACTTGCTCCTGTAGTACTCATAATTTAAAAAAAATACTATTTCAGTATTATTGGCCTTAGCCTTCCTTATTCTCTGAAAAGCTTTTTTTCCCCCTGGTCACTATATGGAGAACATTTTCTTGGCTGCCTCTGCTTTTAACCAGGATCAAACTGACTCCCTAGACCCCACCCATTTTCGGCTATGCTGCTTTTCCGAATTTGTCATACTTTAGAGGCAAAGAGCAAGGAACCTGCCTTTGAAAGATGATTAGCATCAAGAAGGTTAATTTCTATCCAGTGAATTTACAGATTATTTTAAATTTAGAAAAGATGTAATTAATTACATAGTAGAAGAGGATTTTCACAAATTCTTGTTGAATAGGCTAGTGAAATTACAAATGAACTGATTTCATGAGCTGGACTGCAGGGACAATTTTTCCTGCAGTAAGAAAATGAAGTTAGGTACGGTGATGCATGTGTAAAATCCCAGTATTTAGGAGTTAGGAGCAGGGAAATTAAAAGTTCAAGGCCATCCTTAGCTACACAGTAAGTTTGAGGCTAGCATGCATTGCATGGAAAGTAAAGCCTAGTGTAAAGGAGGGCTGACAAGGGAATTTAGTAGTAGCAGGGTGTACAGCCAGGATGTGGGCAATAGCAGGTATAGACTGAGTCTCTTTATGTACTCGCCATATACGCACTGCCCCTCCTGAAAGACAGACTCTGAGGCCAGCAGGAAGAAGCTCTGAAGTTCTGGAGTAGCATCTCTGCACTGACGGCAACATTAGCACTGGGGCAAGACAGTGATACAGAATTAGGTGGAACGTGCAGTTGCAGCTTGCAAACCTGAAAGCATTGATGCTGAGTAACCTTTTTCTTTTACAG
Seq C2 exon
TCGCTGATTGGCTGGAGGAATGTAACACGACTGCTGGTGTTTTCCACGGATGCTGGGTTTCACTTTGCTGGAGATGGGAAACTTGGTGGTATTGTTTTACCCAATGATGGCCAGTGTCACCTGGAAAATAATGTGTATACAATGAGCCATTACTAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010966:ENSRNOT00000014785:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=FE(18.3=100)
A:
NA
C2:
PF0036213=Integrin_beta=FE(11.8=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:
TGTGGAGAAAACTGTGATGCCA
R:
AGGTGACACTGGCCATCATTG
Band lengths:
348-2266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]