DreINT0083255 @ danRer10
Intron Retention
Gene
ENSDARG00000016939 | itgb2
Description
integrin, beta 2 [Source:ZFIN;Acc:ZDB-GENE-110411-4]
Coordinates
chr9:45163540-45164862:-
Coord C1 exon
chr9:45164646-45164862
Coord A exon
chr9:45163746-45164645
Coord C2 exon
chr9:45163540-45163745
Length
900 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
TTTGATATGTTTTTAAACAGGAG
3' ss Score
8.08
Exon sequences
Seq C1 exon
GTCATGGCAAGTGCAAATGTGGCAAATGTGAGTGTGATGACGGCTATGAGGGAACAGCTTGTCACTGCGCTAAATCCGACAATGAATGCAAGATTGACAGCCATGTTTGTTATAACCGCGGTAAATGTGTATGTAACCAGTGCGAATGTGAAAGGGGATACAAGGGACCCTACTGCAAAACCTGTCCTACATGTCAACGTCCGTGTCAACAGTCCGG
Seq A exon
GTAAGAAAACCTTCAAAGCTGCCATCCAAAATAAATTATTCATCAAGCAAAATACACATATTTTCCATCAATGCATAATAGCTGTGAGGGGATTATTACTAATTAATCTCAATCTGTTAGCTAGTCATAAATATATAAATGATTTCCAGGCGTGTCACATCTTAAATAAAAATATACTTTAGTGTTACTAATTATACTGTATGTTCTGTACACTATAAAAAAATGTATCTGTGTTGGGACCACATGACGAAATTAAGTTAACTTAATAGTTTTTACAAAATTAAGTGGATCGAACATAAAACAATTAAGTTGTTCCCCCCAAAATCTCAAGAATTGTTTTGTTTTCAGCTTATTTTAAATAAGTAGTTTGAACAAACAGCAAACATCATTGTTTAAGTGTATGTTATCTATCGCAGAGTTTAAATGATGTGTAAATGTACATAGGAGATAAAAATTAGACAATAATGTACAATTTTGTAAATTTTATAGTCACTGTAGAACTATTTGTAGTATTTTAACAGGAGTAAAAGACTTTTTAAGAGTCTTTATGAGTTGCACTGTAAAAAAGTGATTAGCGAGTAAACCAATTGCCTTAAAAGAAACAAGCTGACTTTACAAAAATAATGTAAGTAAACCCATTGTAACTTGGAACAGTTAAGATGACTTGATTTTTAGAATTATGCTAATTAATTAAAGTGCCTTGGTTGTTTTGAAAAACTTTGTTCCTCTAGCAAGGAGTAGTTTCAATAAACATTTTTTTTTTTGAAGATTATTTCTGATGTTCATGGATTATTCTCTCATTTTGACCTTTATTGTACTGTATATACAAAAGAAATCTAAATACAATACATAAATTAAATATTACATTTTATGCTCTAAATTTGATATGTTTTTAAACAG
Seq C2 exon
GAGCTGTGTTGAATGTTTTGCCTTTCAAAGTGGACCGTTTGAAAAGAACTGTAGTTTAGCCTGTAAGCATCTGACGATTAAGATTGTCGATAAACTGGTAAAGAGTGATTGCAGAGTCAAAGATAAAGAGGGCTGCTGGATGGCTTTTACAATGACAGAAGAACTTGGATTTGACCTCTACTCTGTCAGTGTCCTTAAAGACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016939:ENSDART00000149704:13
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=0.000
Domain overlap (PFAM):
C1:
PF079748=EGF_2=PD(64.5=27.4),PF079748=EGF_2=WD(100=41.1),PF079657=Integrin_B_tail=PU(5.0=5.5)
A:
NA
C2:
PF079657=Integrin_B_tail=FE(86.2=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:
GGCAAGTGCAAATGTGGCAAA
R:
CCATCCAGCAGCCCTCTTTAT
Band lengths:
355-1255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]