GgaINT0046606 @ galGal4
Intron Retention
Gene
ENSGALG00000012479 | RBM43
Description
RNA binding motif protein 43 [Source:HGNC Symbol;Acc:HGNC:24790]
Coordinates
chr7:34600909-34601692:-
Coord C1 exon
chr7:34601494-34601692
Coord A exon
chr7:34601004-34601493
Coord C2 exon
chr7:34600909-34601003
Length
490 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTC
5' ss Score
6.8
3' ss Seq
GAATCTGGCTTTCTCTTTAGTTG
3' ss Score
6.9
Exon sequences
Seq C1 exon
GACATGGGACAGGCTGCTAAATCAGCAAGGACCGTTGTCATCTCTGGTGTTCCAGATGGAGTTCTGAACAATGATGTCATGAGCGACATTCTGGTGATTCATTTCCAAAAGGCAAAGAATAACGGTGGAGATGTGGAAGAAGTGAAGTATCCAACAACGGAAAAAGGAGTTGCATATATAACTTTTGAAGATCAAGAAG
Seq A exon
GTATTCCCACTACTATACCGTAGGAATAGTTCTCCCAGGAATTAGCCTTAGAGCGTTTACTCTAAAACAAGTGATTCTAAATTGCTTACTGGTATTAGGATTTTATGTGTCTGGGAGACCAACACCTCTATTTTAGTCAGAGTTGTAGGATTTTCCTTCTGTTCAGTGAAGAAAAGACTCTGAAGAGACTTTGCACAAACTTTTGTCTGTTTCTAGAAACAAACTTAAGCACTGCATAACATGATCTTTGTAGTCAGGCCTTTGGGAGCAAATCTCTGACAATTAATGTTCTGAGGAGACAGGCTTCTGTCTCTCTGAACCATTTCGACTAATGCAAATATATTGGGCAAGAGAATTGGATCACCTGTGTGTATGTATGGAAATTTTAGGGAAAGCATCAAGAGGGAAACACTCACACAATGTTGCACTGTCAGACTGGCAATAACACATTATCCTACTGCCAAACAAGTGAATCTGGCTTTCTCTTTAG
Seq C2 exon
TTGTAGGGAGTGTTCTACAGAAGAATGAGCATCGACTAGAAGACAGGAGGCTGCCCAGATACTATCCTCTGAAAGTAACTGCTTACTGTGAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012479:ENSGALT00000020389:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.104 A=NA C2=0.031
Domain overlap (PFAM):
C1:
PF072928=NID=WD(100=65.7),PF142591=RRM_6=PU(75.3=82.1),PF072928=NID=PU(11.5=13.4)
A:
NA
C2:
PF142591=RRM_6=PD(23.3=53.1),PF072928=NID=FE(39.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGACAGGCTGCTAAATCAG
R:
TCACAGTAAGCAGTTACTTTCAGAGG
Band lengths:
286-776
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]