GgaINT1026424 @ galGal4
Intron Retention
Gene
ENSGALG00000001917 | SSC4D
Description
scavenger receptor cysteine rich family, 4 domains [Source:HGNC Symbol;Acc:HGNC:14461]
Coordinates
chr19:4224502-4226022:+
Coord C1 exon
chr19:4224502-4224813
Coord A exon
chr19:4224814-4225615
Coord C2 exon
chr19:4225616-4226022
Length
802 bp
Sequences
Splice sites
5' ss Seq
GAGGTGCGT
5' ss Score
8.42
3' ss Seq
GGATGGTGAGCGTCCTATGGGCG
3' ss Score
-10.2
Exon sequences
Seq C1 exon
GTGGCGGCGTGCGGTTGGCGAACGGCAACGGGAGCTGCCGCGGTCGGGTGGAGGTGCGGCACGGCGGGACGTGGGGTACGGTGTGCGACGACGACTGGGACTTCCCCGACGCGCAGGTGGTGTGCCGGCAGCTGGGCTGCGGGCCCGCCGTCTCCGCCACCGTCCTGGGTTCGTTCGGGTACGGCAGCGGGCCCGTGCTGCTGGATAACGTGGGGTGCGACGGGCACGAGGCGCGCCTGGCCGACTGCTTCCACCTGGGCTGGGGGCAACACAACTGCGGCCATCACGAGGACGCGGGCGTCGTGTGCCGAG
Seq A exon
GTGCGTGGGCCGAGCATCGCCCCTCCCGTCCGCTCCCATCCGGGGGTGGGATGTGGGGATGGAGTGCGGTCCTAAGAGGGCGGTGTTGCCGGCCCAGGTCCGGGCGGGGGTCCGCTTTGCACAAAGCTTAGGGAAAGGCTCTGCAGCAGAGGGGCGACGGGGGGCACAGCCCTGAGCTCGAGGACCTGATGGACGCATGTAGGGTTTGGGGGGTCCTGGGTAGAGCCGTGGGTTGGACTCGGTGATCTCCGGTTGGATATTAGGAAGAATTTCGTCTCCAAAGAGTGGTGCTGCAGTGGCACAGCTGCGCAGGGTGGTGGGGGAGTCACCAAACGTGGAGGTGTTCCAGAGCTGTGGGGATGTGGCACTGAGGGCAGTGAGCAGTGGGCACAGTGGTTGGACGTGGGGATCTTGGAGGTCTCTTCCAAACTCAGGGACTGTGATTCCACGGTTCCGTGAGCCCCGTGGGTGCCTTCTGCCTCGGGATGCTCTGCGGCTCTGTGCCTCAGGGAGGACAGCAGCACGGCAGTGTTGTGGCTCGGTGAACACATGGGTGCTGTGTCTTCTCTCACGTGTGCTCCCTAAGCACGGCGCCCACATTACTCAGCTCCTTTCCCCTGCCAGCCCCGTGCCACGTGCACTCTGAGCTGGTCCTGGGGAGCACAGGATGGCCCTGAATCACCTTCCCCCCATTTCCCTGCCGCATCAGGTGCTGATGACTCAGGAGACCACTTCCAAGAAGCCACTGTTGCCACCACCACGTCGGCCCCGACCCATCTGGAGGATGGTGAGCGTCCTATGG
Seq C2 exon
GCGCTGGCGTGGAGAAGCGAGGCTCGCCCTGGCCCGGCCTGGCCGGGACGAGCCCATTCTCCTCCACCCCATCCCAATGTCCCACCGCAGGGTTCTTGCGCCTGGTGAACGGCAGCCATCGGTGCGAGGGCCGCGTGGAGATGTTCTACCTGTCCCAGTGGGGCACGGTGTGCGACGACGCCTGGGACCTGCGGGACGCCGAGGTGGTGTGCCGGCAGCTGGGCTGTGGGAGCGCCGTGGCGGCGTGGGGGGAGGCGCACTACGGCCCCGGCACCGGGTACATCTTCCTCGACAACCTCAAGTGCAAGGGCAGCGAGCCCGCACTGCTGCGCTGCTCACACATCCGCTGGGACGTCCACAACTGCGACCACTCCGAGGACGCCAGCGCGGTCTGCAGCCTCCTATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001917:ENSGALT00000040256:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=93.3)
A:
NA
C2:
PF0053013=SRCR=WD(100=72.1)
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:
CAACACAACTGCGGCCATCA
R:
TTGCACTTGAGGTTGTCGAGG
Band lengths:
353-1155
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]