DreINT0083216 @ danRer10
Intron Retention
Gene
ENSDARG00000071863 | itgb1a
Description
integrin, beta 1a [Source:ZFIN;Acc:ZDB-GENE-060803-2]
Coordinates
chr24:1122939-1124734:-
Coord C1 exon
chr24:1124502-1124734
Coord A exon
chr24:1123106-1124501
Coord C2 exon
chr24:1122939-1123105
Length
1396 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGTGTTTTGTGATTGTCCAGAGT
3' ss Score
6.21
Exon sequences
Seq C1 exon
GGAGTGTGTTCAGTGTCGTGCGTTCGGCACCGGAGAGAAGAAGGACACCTGTAAGCGCGACTGCAGCTACTTCAACCTGATCGAGGTGGAGGATCGAGACAAACTCCCGCAGCCGGTGCAGGCCTTTCCACTAATGCACTGCAAGGAGAGAGATGCGCGAGACTGCTGGTTCTACTACACATACGCCGTCAACAACAACACAGAGAAGGAGGTGCACGTCGTCAAGACCATGG
Seq A exon
GTGAGTCCACAAAATCACTATTAAATCCCTCTGAAATCATAACCTAAATTCCACTAAAAATTAAATTACAGTCCGTTTGAAATCAGAATGAAAATCCTGCTGAAATAAAAATAAAAGTTCCCCAGAAATCAAAATTAGAGTCTGTTCGAAATCAAAATAAAAATCCCCCTGAAATAAAAATAAGTCACAGTGAAATCAAAATTAGTCTACCTTAAATCAAAATCCCACTGAAATCCACTTTAAATCACCCTGTAATCAAAATCAGTGTACCCTAAATTAAAATTTAAATCATGACTAAAGTTCCCCTGAAATAAAAATTACAGTCCGTTTGAAATCAAAAGGAAAATCCCCCTTAAATAAAAATCTAAATGCCACTAAAATCCAAAATTAAAGTCCCCCTAAAATCAAAGCTAAGTCTGCCTAAAATCTAAATTAGAGTCGCTCAGAAATCATAACTAAGGCTCTACTGAAATCAACAATACAGTCCATTTAAAATCAAAATGATATTGATAAAAATAAAAATCAAATTCTTTGATATCAAAATAAGTCCATTTGAAGTCAAAATGAAAACCTCCTGAAATTAAAATTAAGTCTCAGAGCTAAAGTCCACTGAAATTAAAAATGTTGTGAAATCAAAATCCCACTGTAATCTTAAATTAAAGTCCCCCTGAAATCAAAATTAGTCTACCTTAAATCAAAATTAAAGTGCCCCTGAAATCAAAGCTGAGTCTACATGAAATCAAAATTTGAATCCCCCTGAAATCCTATTTAAAATTAAAAATTAAAGTAAAACAAAAGTTATATAAAATAATCATTTAAATAAAAGTCTCCATGAAAGCAAAATTAGAAAACCCCTGATATCAAGCTTAGTCTGTTTAAAATCAAAAATCCTAGTAAGGCCAAAGCTAAAGTCCATTTAAAACAAAATATCACTGAAATTCTAAATTAAGGTGCCTCTTAAATCGGAATTAGCTACCTTAAATCAAAATTAAAGTCCCCCTGAAATCAAAGCTGAGTCTACATGAAATCAAAATTTAAATCCCTCTGAAATCCTAATTAAAAATAAAATTAAAAATTAAAGTAAAACAAAAGTTATATAAAATAATAATTTAAATAAAAGTCTTAATGAAAGCAAAATTAGAAAACCCCTGATATCAAACTTAGTCTGTTTAAAATCAAAAATCCCAGGGAGCCCAAAGATAAAGTCCATTTAAAACAAAATATCACTGAAATTCAATATTAAAGTCCCCCTTAAATCAGAATTAGTCTACCTTAAATCAAAATTAAAGTCCCCCTGAGATCAAAATTAGATTAGGGCAATTGCGATCCTACAGTTAACATGAACATGATTACCAATAATAAGTGGTGACTGTTGCTGTGTTTTGTGATTGTCCAG
Seq C2 exon
AGTGTCCGCCGGGTCCAGATATCATCCCCATCGTGGCCGGTGTAGTGGCAGGAATCGTGCTGATCGGTCTCGCTCTGCTGCTCATCTGGAAGCTGCTCATGATCATCCACGACCGACGTGAATTCGCCAAATTCGAGAAGGAGAAGATGAACGCCAAGTGGGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000071863:ENSDART00000039700:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.006 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF079657=Integrin_B_tail=FE(87.6=100)
A:
NA
C2:
PF079657=Integrin_B_tail=PD(6.7=10.7),PF087256=Integrin_b_cyt=PU(53.2=44.6)
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:
AAGAAGGACACCTGTAAGCGC
R:
CCCACTTGGCGTTCATCTTCT
Band lengths:
358-1754
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]