BtaINT0141310 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003020 | SSC4D
Description
scavenger receptor cysteine rich family, 4 domains [Source:HGNC Symbol;Acc:HGNC:14461]
Coordinates
chr25:34938715-34940479:-
Coord C1 exon
chr25:34940314-34940479
Coord A exon
chr25:34938751-34940313
Coord C2 exon
chr25:34938715-34938750
Length
1563 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TCTTCCTCACTCTGTTCCAGCTG
3' ss Score
9.78
Exon sequences
Seq C1 exon
ATGGGACCACTGGAAAGACCACCCATTGGCTGGACACACAAGGAAGCAGAGATGCACACTGGTCCCCAGCCTGATGAGAGGAGCAGAGGACGGGGGTCCGGAGACAGGAGCACTGCCCCTCCCCCTCTCCCCCCAGCCCTGTCCTTCCTCCTCCTATTGCCACTGG
Seq A exon
GTGAGTGCCTCCCAACTCCCCTGACCCTTCCCCTTCCCTTTTCTGACTCTCAGCTTTCCCAGTTGTAAAATTATGGTGGGACATGGCCTGTAAACGAGGTGTTTTCCAACATTCTTTCCAGCTCTGCCATTTGCCCCAGGTTGATGAAAGCTAAGGTCTGAGTTGGGGGAGTGGAAGGCTCAGTGTTAAAGGCTAGAGCTCGATGCACACAGAGTCTAGGCAGTGAGGATACTGGAAATAGGGAAGGAGCGAAAGGGCATGGACTCACCAACGGCTGTTGGAAAACCAGCTGGTAGAACAGATGGAATCAAACAACCTAGGAACTAACCTAACTTAGGAAAAAAGAAACTGACTCTCAGTTTCTTCATCTGTAAAATGGGTTCACTAGTACATGCCTCAGAGGTTGTAAGGTAAGGTATGGGGCTGTGTCTGACAAGCCTGTGCACAAATGAAGGGTACTATGGGGTATTAACTTCTCATGCCAGGCCAGTTTCCTTCTTAGGCCACGTGCTCAGAATTGTTTGGTGAAGAGGAGTGTGGCTATCTGGGTTAGAATTTCTGCTCCACCCTTTATTTGCTTTGTGGCCTTGAGCAAGTGGCCTGACCTCACTAAACCTGAAGTTTTCCCTTCTGCAAAATCTAAGCTGCCTCATAAGTTGTCCTAATGATTAAGTGAGCCAGGCCACATAAAGCAATGAGCACAGTGCTGACATATGCAGAAGCAGAAGGACTGATAGGGACTTCCCTGGTGGCCCAGTGGTTAAGACTCTGTGCCTCCAATGCAAGTGGTGTGGGTTCTATCCCTGGTCAGGGAACTAAGACCCCACATGCCACAAAGCATGACCAAAAAACCAGAACCAAAAAAAAAAAAAAAGAAACCCAAAGGAAACAGAAAGACTTACATAGGTAAACTCTTTAGTGGGAAACCAGAATGAAACCCAAAGTTAATTTACACCCTTAAGGCAAAGCTGGGGAGTAACAGACTCTGGGCAGGGAGCTCTGGGGAAAACCAAGATGACACAGACCTGGCCACGTCACTGGGCAGAAGGCCTGGAAAGGGGTATGTATATGGCATCCAGAGATTCAGAGGAGAAAGACAGCCCTTTTAGCTGAGAGCTCCAGGAAGGCTTCCCATAGGAGGGGGCTCCATCTGCAGGGCTGTAATGAGCAGGGGGAGCAGAGGAGACAGCAAGATTACAGACCTGGTGACCAGACTGATGCAAGATTAACAAGGAAGGTGAGGCTACTCAGAAGATCCTAGAAGGCTTTGCAGAGAAAGTTCAGGGTCCAGGACTTCTGCAGGAAATGGGGAGAGGAATTCAGCAGTGGAATGGGATCAGCCTGTCTGGGTCTCAGGCAGATCTCTCTGGGGCGGCCCATGGACCAACCGGCGAGGGATGAAGCCAAGAGGCCAACTGGGGCAGTCAGGGGCTTTGGAAGCAGGGGTGGTGACGAGGAAGAGGGTGATGGTGAGGACTTGAGGGGAGGGTTGGAGGGGAGGCTGTGTTCCTGGGGCCAAGGGAGGGGGCTGAGGGGCCAATTCTCTTCCTCACTCTGTTCCAG
Seq C2 exon
CTGGTGCCCTACAGCCCACCTCACTGCCCTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003020:ENSBTAT00000003928:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCACTGGAAAGACCACCCA
R:
CTGGAAAGGGCAGTGAGGTG
Band lengths:
198-1761
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]