DreINT0083341 @ danRer10
Intron Retention
Gene
ENSDARG00000002494 | itgb6
Description
integrin, beta 6 [Source:ZFIN;Acc:ZDB-GENE-100812-2]
Coordinates
chr11:11002449-11004083:+
Coord C1 exon
chr11:11002449-11002528
Coord A exon
chr11:11002529-11003884
Coord C2 exon
chr11:11003885-11004083
Length
1356 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
TATTCAAAATATTTATTTAGAAC
3' ss Score
4.02
Exon sequences
Seq C1 exon
GGACGTGTTCTCAGATCAGTGCTCTCTCTTGTGACGATTGTCTGCAGCTCGGGCCACAGTGCGCTTGGTGCACACTACAG
Seq A exon
GTAACAGCTTCTCCTCAGCGCTTTTTGCTTTCAAAGTTGTTTCATGATATGATTTAACATTAGAATTGCATGGTGTAATATAATGGAGACATTTTTGTTTAAATTCTCCTTCTTGTCTGGTAAGAGGACTGAATAGTTAGAAAATAGTTTGTCCCATTTTGTCAGTTTAAGTAGCTGTTAATTTTATTGTTTTGTTCTGTTTATTTAATGTTTTTATGTTTAGTGAATAAGCTGTATTTCGGTTTTGTGACCTGTGAAGGGACCAAAGACAAACTTCTAATTGATAATGTGATGAAAAATATTATATATGTGCTTATTTTGTGTAGGCAAACATAAATCACATACACAGTCACATACTGTACAGACCTTTAAAATCTGAAACACTAGGGTTACAATATTTAACACTTTTAAAGGGTCAAACTGCATATAATATAATATAATATAATATAACATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATATAATACAACATTTTGAATAAATCACACTACAAATATTACATATAACACAATTAAAAAATTAATTCATTCATTTTCTTTTCGACTAGGGTTGCCACAGCGGAACGAACCGCTAACTTATCCAGTATATGTTTCACACAGTGAATGCCCTACCAACTGCAACCCATCACTGAAAAAAACAAAACAAACTTGTGTATATATATATATATATACATACAACAGTTCTGTCTAGTTCTCGAATCTGACTGGCTGATAGCTGTGATACAGTTAAGTTATATCAGCAACCGTACAGCCTCTTTACCCTTTGTGTATTACTCCGCCTACATACAGCAAGCAACAAGCAGACACTACAGATCTAAAGTTTAAAAGATGCTTGCTCAGCTGTTTAACTGTCAGCTTATGATTTGAATCCAACACGGAAGAAAGTAGTTCCTCATACGAAAGGGTTTTTGAGACTCTCCATGTTTAATTTTGTTTCATATACACAATTATGCCGTCAAACTGTTGTATAAACGCAATATCACACTCGTAGCAGTGATATTGGCCTGCGGCCTCGTGCCAACACAAGCCTTTCACCAGTGCTGATATACAGCCATATCGCACTGCTACTCGTGTGATATTGCTCATATATATATATATATATATATATATATATACATATATATATATATACATATATATATATATACATATATATATATATATATATATATTTTTGTAAAGCTTAAATTATTAGTGCTGTTTGTGTTTAAGTTAATTATATCCCTGTGGAACACTGTAAAGTAATAATTAATCCAAAGTAATAACTAATCCAAAAGACTAACCAATATTCAAAATATTTATTTAG
Seq C2 exon
AACTTCACAGATTTTTTCCCAGTTGATGAGAGATGCGACACACCGGAGGCTCTTCTCCAGAAGGGATGCTCTGGCGAATTTGTGGAATTTCCCGTCACGAACGTCAAAGTACTGAAGGATCAAGGTTTAGGAAAGAACTCAGGCCACACCAATGTGTCATACATCGCACCGCAGAAGATGCGCCTCCAGCTTAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002494:ENSDART00000065933:2
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:
PF0143720=PSI=PU(48.1=92.6),PF0036213=Integrin_beta=PU(9.0=63.0)
A:
NA
C2:
PF0143720=PSI=PD(48.1=37.3),PF0036213=Integrin_beta=FE(34.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACGTGTTCTCAGATCAGTGC
R:
GCTGGAGGCGCATCTTCTG
Band lengths:
270-1626
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]