BtaINT0141313 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003020 | SSC4D
Description
scavenger receptor cysteine rich family, 4 domains [Source:HGNC Symbol;Acc:HGNC:14461]
Coordinates
chr25:34935998-34937254:-
Coord C1 exon
chr25:34937177-34937254
Coord A exon
chr25:34936313-34937176
Coord C2 exon
chr25:34935998-34936312
Length
864 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
GTTCCCGCCCCCATCACCAGGTG
3' ss Score
8.73
Exon sequences
Seq C1 exon
AATTCTTGCCCACGCAGCCCCCAACAAGGAGAGTGTTAACCAGCAGGGAACCCCCTACAACGCCCCAGAATGGAAAAG
Seq A exon
GTAAGCAAAGGCAATGTGGGGGACCACCTGGGTCTTAGGAGAGGGATCCAAGAGGAATCTCCCAAATCCTACCCTAGGCAGTGGGAAGAGAGGGATTACTGATGGGTGAGTTTGGTCATTCCCTCACCCCTGCTCTGCCCCCTGCACCCCCACCCCGCAGGCTGCTCACTATCTGGATAAGGAAAGAGGATTCATTCTAGTGAGATGATAGAAATAGTAGCATAAGGTTGGAGAAAATAAAAGAGGTGGGCTAGTGTTAGTCATTCAGTCGTGTCCAACTCTTTGTGGCCCCATGGACTGTAGCCTTCCAGGCTTCTCTGTTCATTCTCTAGGCAAGAATACTGGAGTGGATTCTCATTTCCTTCTCCAAAAGAGGTGGGGGCTGAAACCTAATCCAATGGGAGAGTGAGATATACTATATATAGAAATGCTGATAATCATCTTAGAGCAAGAAAATGAAAAACGAAAAATTCTCTTAAAGGACAGATAAAAAGGCAAGGGAGTCCAGAGGAGGAAGAGGATCCCACTCATCAGAGATTAGAGAGGGCTTCCTGGAGGCAGAGTTGTTTGTGAAGTAAGGAATCAGCACATTCTATACGGTTTAGGAGAGCGTGGACAAGGGCAGGCTGAAAGTGACAGAGTTATAGGATTCTATCCTCAGATCCCCAAAAGCGCCCCTAATCTAGACTGTGAGGAGGCAGTGCTTTGGGGGTAAGTAGGTGAGCAGGTCTTCCTGGGTGTTAGGTCCTGGGACACCATGTATTGTGGGTATGCAGAGGGCCTGGGGCAATAGGAAGACCACTGGATTGGGATGGGCAGCAAAGCCCTGGGGGAGATGCTCCTGGTTCCCGCCCCCATCACCAG
Seq C2 exon
GTGAGGGCAGCGTGCGCCTGGTGGGGGGCGCAGGCCCGTGCCAGGGCCGAGTGGAGATCCTGCACGGTGGCCTGTGGGGCACCGTGTGTGACGACGACTGGGGGCTGCCGGACGCAGCCGTGGTGTGCCGCCAGCTGGGCTGCGGGGCGGCCCTGGCAGCCACTACCAACGCCTTCTTCGGCTACGGCACGGGGCACATCTTGCTGGACAACGTGCACTGTGAAGGCGGCGAGCCCCGTCTAGCAGCCTGCCTGAGTCTGGGCTGGGGCGTGCACAACTGCGGGCACCACGAGGACGCCGGCGCGCTCTGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003020:ENSBTAT00000003928:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.704 A=NA C2=0.028
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCCCAACAAGGAGAGTGTT
R:
CAGTTGTGCACGCCCCAG
Band lengths:
342-1206
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]