DreINT0083259 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45174306-45175605:-
Coord C1 exon
chr9:45175514-45175605
Coord A exon
chr9:45174499-45175513
Coord C2 exon
chr9:45174306-45174498
Length
1015 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
CTGCGTTTTTCAAACCACAGAAT
3' ss Score
6.28
Exon sequences
Seq C1 exon
TCTACACACAGGAGCAATGCTTAAAAGCTTCAGTAAACACATGTGGAGACTGCATCAAGTCTGGACCTGGCTGTGCATGGTGTAAAGAGTTG
Seq A exon
GTAAGTACAGTTAATGGTTCTATTTTTAATACTGCTGAAATGCATTTTCATTGGTGAATCTGCCCTCATAAAATGACTGACTGTTTAATGACAGTTTAAATTTATGAATATATTTAATGCTGATTTATTATATAGCATGATGTCTAGCCACTTTACAGCTTACTGTCCAAATATAATGCATTAAGATGATACATAAAGTGGGCAGTTTGTTATTGCATTCACCTAGTACCTAGTTGGACCCCCTTTTGCCTTCAGAACTGTCTTAATCCTCATGCAGTTGCTTCTGATTTATTGGCTGCACATGCATGATGCGAATCCCATTCCACCACAACCCAAAGGTGCTCTATTGGATTGAGGATCTGGTGACTGTGGAGACCATTTGAGTAAAGTGAACTCATTGTTATGTTCAAAAAAACAGTCTGAGATGATTCATACTTTATGACATGGCACGTTATCTTGCTGGGAGTAGTCATCAGATGATGGGTACACTGTGGTCATAAAGGGATGGACATGGTCAACAACAATACAGTGACACAATGCTCAAATGGTACTAATGGGCCCAATGTGTGCTAAGAAAATCCCCCACATCATTACACAGCCATAACCAGCCTGATCCGGTGATAGAAGGCAGGATGGATCCATGCTTTCATGTTGTTGACGCCCAATTCTGATAAGAAATTTGTATTAATGAGCAGTAGGACAGGTGTCCCTAATAAAGTGGCCGGTGAGTGTATTTAGAATGAGCTGAAACAACAACTCTTGATATTATTTGGGACAACTTAATTGTTTTATAGGTTGTTGCTAGATCGGATATGGTTGCTGAAAATTTAACAATTATATATATTTTTTATTAAATTTCCCATTTATTGTATTTTATTAACCTTTACCCCCACCCCAACCCTAAACCCAACTATCACAGTAATGTAAAAACAGTAGCTGCATTTAAATGAGCTGAAAATATAATGACTGGCTGGCATGTCACTCCCTTCTACTTTCTGCGTTTTTCAAACCACAG
Seq C2 exon
AATTTCACCAAGACTGGAGAGCAGGAAGCAGCACGTTGTGACACTGTCAAGTTGCTTTTAGACAGAGGATGTAGCAAAGAGAACATCATAAATCCTCAAAACATTTTTCAAAATGTTGTGAACAAAGCTCTGGTTGCTGGTAAAGACCCAGTGCAAATCCAACCCCAAGAAATACAACTCAATCTTAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:3
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=0.046
Domain overlap (PFAM):
C1:
PF0036213=Integrin_beta=PU(4.1=54.8)
A:
NA
C2:
PF0036213=Integrin_beta=FE(15.3=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:
TCTACACACAGGAGCAATGCT
R:
AAGATTGAGTTGTATTTCTTGGGGT
Band lengths:
278-1293
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]