DreINT0083074 @ danRer10
Intron Retention
Gene
ENSDARG00000069946 | itga6b
Description
integrin, alpha 6b [Source:ZFIN;Acc:ZDB-GENE-050320-5]
Coordinates
chr1:30237382-30238312:+
Coord C1 exon
chr1:30237382-30237595
Coord A exon
chr1:30237596-30238118
Coord C2 exon
chr1:30238119-30238312
Length
523 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAAA
5' ss Score
3.28
3' ss Seq
TGAACTGATTCTTAAAACAGGTG
3' ss Score
6.67
Exon sequences
Seq C1 exon
GTTTCTCTTTGGATTCTGGAAAAATGCTGACTAAGAGAGGTCAGTTGACCATAGTTGCTGGGGCTCCAAGAGCCAATCACAGTGGGGCAGTTGTGCTTTTAAAGAAGGATGAGGCTAAATCCTCCTTGTTGACGGCTGAGTACACCCTAGAGGGTAGTGGACTTGCCTCTTCCTTTGGTTATGACCTTGCAGTGCTTGACATCAATGGAGATGG
Seq A exon
GTAAAAATTATACATTATATTAATTTATTTTATTTTAATAGAAATTGGGATTATTTTGCCTTATTTGTATTTTTATTGATATTTTTGTGATTTAGCTTTGTGAGATTAGCTATGTTTATTTTTTTACTTTTTCATAATCATTTTAGTTATCAGTTTTGTAATGTTGTAATGTTCTTTTACACATCTTTTTTTTCTATATATGTTTATTTTAACCGAATTTTAAAGTTTAATTAATTAAAAAAAAAACATTTTTGTTTTATTTATTCATTTATTTATTTGTTTATTTATTTATTTATCTATTTATTTATTATTTATTCATCTTATCACATTTTTACAGCTTTATTAACAAAAGATCAATATAGTTTAATAGATGTACTGCAAGTTTTTTTTTTATCTATATTTTTAATATAATTTAATTAAAGTATTTCTGTGTTAATAACAAAACATTTAAGTTTTATTAACCTTTAGTTTTATAAATACACTATTCCAGAAGCATAATTATTTGAACTGATTCTTAAAACAG
Seq C2 exon
GTGGCAAGACATTGTAGTTGGAGCACCTCAGTACTTCATTAAAGATGGTGATATTGGTGGAGCAATCTATGTTTACCTTAACGAGGAAGGAGCTTGGGACAAGATTACTCCAAAGAGAATTGATGGACCTGCTTATTCCATGTTTGGTTTGGCTGTGGAAAACATGGGAGATGTGAATCTGGATGGATATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069946:ENSDART00000102210:6
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:
PF135171=VCBS=PU(25.0=31.9)
A:
NA
C2:
PF135171=VCBS=FE(70.7=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:
GTTGACCATAGTTGCTGGGGC
R:
TCTCCCATGTTTTCCACAGCC
Band lengths:
342-865
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]