GgaINT1026427 @ galGal4
Intron Retention
Gene
ENSGALG00000001917 | SSC4D
Description
scavenger receptor cysteine rich family, 4 domains [Source:HGNC Symbol;Acc:HGNC:14461]
Coordinates
chr19:4221300-4221832:+
Coord C1 exon
chr19:4221300-4221605
Coord A exon
chr19:4221606-4221760
Coord C2 exon
chr19:4221761-4221832
Length
155 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
ATCTCTCATTCCCTTTCCAGAGC
3' ss Score
10.96
Exon sequences
Seq C1 exon
AGCTGCGCCTGGCCAACGGGCCCAGCCGGTGCCAGGGCCGCGTGGAGATCCTCTACAACGGATCCTGGGGCACGGTGTGCGACGACGACTGGGACATCGTAGACGCCAACGTGGTGTGTCGCCAGCTGGGCTGCGGCCACGCCATCGCCATGCCGGCACCCATGACCTTCGGCCAGGGGAGCGGGCCCATCTTCTTGGACAACGTGGACTGCAAGGGCCAGGAGGCGGCACTGAGCGAGTGCTGGAGCCACGGATGGGGCGTCCACAACTGCTACCACTACGAGGACGTGGCTGTCGTCTGCAATG
Seq A exon
GTAATGAGGCTCGGTTCCCTCAGGGCCAGCATGAGGCCCACAGAATGTTATTGTTTGTATTAAGTGTATCGTCACGGCAGGGATCCTGGCTACAGCTCGCTTCTGGGAGGCTTTCTGCAGGCAGAAATCGATGCCATCTCTCATTCCCTTTCCAG
Seq C2 exon
AGCTTTCCCCCACATCAGCAAGCGAAGGACCGACCAGCAGGACTGCCACGGCCTCGGTGCAGAACGGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001917:ENSGALT00000040256:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.039 A=NA C2=0.480
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=95.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGACGACTGGGACATCGTAGA
R:
CTTGCTGATGTGGGGGAAAGC
Band lengths:
246-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]