BtaINT0141317 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003020 | SSC4D
Description
scavenger receptor cysteine rich family, 4 domains [Source:HGNC Symbol;Acc:HGNC:14461]
Coordinates
chr25:34931163-34932434:-
Coord C1 exon
chr25:34932123-34932434
Coord A exon
chr25:34931232-34932122
Coord C2 exon
chr25:34931163-34931231
Length
891 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTCTGTCCTTGCTGAACCAGGTC
3' ss Score
8.52
Exon sequences
Seq C1 exon
GCGGGCGGCTGCGGCTGGTAGGTGGCCCAGGCCCGTGCCGCGGTCGCGTAGAGGTGCTGTACGCCGGGGGCTGGGGCACCGTGTGCGATGACGACTGGGACTTCGCGGACGCGCGCGTGGCCTGCCGCGAGGCGGGCTGCGGGCCGGCGCTGGGCGCCACGGGCCTTGGCCACTTCGGCTACGGCCGCGGCCCCGTGCTGCTGGACAACGTGGGTTGCGCCGGCACGGAGGCCCGCCTCAGCGACTGCTTCCATCTGGGCTGGGGCCAGCACAACTGCGGGCACCACGAGGATGCGGGCGCGATCTGCTCAG
Seq A exon
GTGAGGCCGCAGCAGGACCACAGGTGCACTGCGGCTCAGGCGAGGCTGAACGCCTTCTGGGAAGTGGGCGGGGCCCCGCGCAGGCGCTTACTTAGGCATTGGCGGGGTCTGCTGTGAAGTAGGCCGTGGTGCCGGCGGGAAGAACAGGCTCTGAGGAATGGGCGGGGCCTCACGGAGGCAGGCTCTGGGGATGGGCGGAGCCTCGCGGAGGCACGCTCTGCGGCGCGGGCAGGGCGGGGTTCGTTGGGAAATGGGCGGGGTCGCGCGTGAGCGCTCACCGCGGCACTGCAGCGTGAGCGCGGCGGGAGAGTGCTCACGCTCCGCAGTAAGAGGTGGAGCCCACCATCGGGTGGAGCCCACTCGCTCTGCGGCTGCGCGGCATGGGCGGGGCCGGGAAGGGAGCGCCCTCTGCGGCAGTGCGGGGCGGGGCCCGAGCAGAGTCCGAAGTGCCGGAGCTCAGAGTGGGAGAGTCAGTCAAGGGCGTGGTCCGGGAGCTTTTGCTGTGCTGCGTCAAGGATCCGAAAAGCTCTAGTTAGCAACGAAAGTTGATCAGCTTTCGGGGAGCATACGTTTGTCCCTTGGGAAGTCACTGGAAAAGGGATAGTTGCAGAGTCCGACACATTTAAAAATGCGTCTCTTTATTGACGGATGTGGGAATTGATATTTTCGCCCTTGTTTGGTGCCCTGGTGGTAGCTTTGGCCACAGAGGGCTCTGCTTTGGGCCCAGAGTGAGAGAAACACAAACCCCGTTTCTGTTCCAAGGAGTGGGGGCCTATGAAGCCCTTTCTGATCCTAGATCAGGCTTCCCTTGGAGGGTAAGAGGTGACCTGGTCTCAAGGGACTGGTTCCCTAGTATCACAGCCACCTCTTTCTCTGTCCTTGCTGAACCAG
Seq C2 exon
GTCCAGATGAGCTAGTCCAGCAGGACGGTGCTGAGACCACCCGGGTACCCACTCCTCGGCCCAGGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003020:ENSBTAT00000003928:8
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=0.667
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=93.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGTAGGTGGCCCAGGC
R:
CCGGGTGGTCTCAGCACC
Band lengths:
342-1233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]