DreINT0136679 @ danRer10
Intron Retention
Gene
ENSDARG00000092989 | si:ch211-161n3.3
Description
si:ch211-161n3.3 [Source:ZFIN;Acc:ZDB-GENE-041210-102]
Coordinates
chr4:10963948-10964590:-
Coord C1 exon
chr4:10964276-10964590
Coord A exon
chr4:10964179-10964275
Coord C2 exon
chr4:10963948-10964178
Length
97 bp
Sequences
Splice sites
5' ss Seq
CAGGTCACT
5' ss Score
3.41
3' ss Seq
TTTTGACTCTGATTTAATAGACT
3' ss Score
5.35
Exon sequences
Seq C1 exon
CTCACGTTCCTCTCAGACTGCGTGGAGGGGGCGGCCGGTGCTCTGGAAGGCTGGAGGTGTATCATAACGCTGTGTGGGGCTCAGTCTGTGATGATCTCTGGGACATCAGCGATGCTCAGGTGGTCTGCAGGCAGCTGGGTTGTGGAGCAGCACTGAGGGCTGATGGGAATTCAGCCTTTGGTGCTGGTGAAGGTGTTGTGTGGCTGAACAGAGTCCAGTGCAGAGGGAATGAGCTTCACCTGTGGGACTGTCCTCTCTCCCTGAACAACCACACTGACTGCTCCCACAAAGAGCACGCTGGACTCACCTGTGCAG
Seq A exon
GTCACTGACAGATTTTTTAATCATTTTAGTGCTAGTAATTATTATATATTTTTTATTTAAATCAGTCATTTGCTTGGTTTTGACTCTGATTTAATAG
Seq C2 exon
ACTTACCAGATATATCAGCGTCCACTACTCCCGCCACATCAGCATCATCTTCTGCTGCAGTTTCTCAGACAGTGAGCTCAACATCAGTCTCTCCTCCACAAACTCATCCAGAAACTGGTCCAGAAACTCATCCAGTCCCCCCAGTGGTGGTGATTGTACTGGGAGTTGTGCTCTTACTGCTCTTAGTGCCGCTGCTTATACTGATTCAGCAGAACAGAGTGATGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000092989:ENSDART00000136440:14
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=0.449
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=92.5),PF151021=TMEM154=PU(11.2=15.1),PF0110213=Glycophorin_A=PU(9.8=10.4)
A:
NA
C2:
PF151021=TMEM154=FE(53.8=100),PF0110213=Glycophorin_A=FE(68.8=100),PF153451=TMEM51=PU(42.0=87.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGTTGTGTGGCTGAACAGA
R:
AAGATGATGCTGATGTGGCGG
Band lengths:
175-272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]