BtaINT0141443 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113457781-113458845:+
Coord C1 exon
chr4:113457781-113457890
Coord A exon
chr4:113457891-113458676
Coord C2 exon
chr4:113458677-113458845
Length
786 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
AGACACCCCTATGCTCGTAGCTT
3' ss Score
2.03
Exon sequences
Seq C1 exon
GCATCATAGTGCAGGGGGCTGGGTCCTCAGACTGGCTCCAGGTCAGCAGTGATGGTCTACACTGGCACAGCTATCGTGACATCCAGCCTGGCACTCAGCCTGCACCCCAG
Seq A exon
GTACCACCCACTCGGGCCCCCTGGACCAGTGGCCCACCATGCCCTTTTGTGTGGGGCCCACAGTCTATGTTCCCAAGGGGTTTCTTGTTTCTGGAGGGACATTTCCTACTTTAGAGGCTTGTTCAGCACCTGTTAGTAGCAGGGACAGTGTTCTGTGGGGCAGAAGAGCCACAGTCGAAAGGGCATCAGACACGATCGAAGTGGCTCAGATGGGGGGCGGCTGTGAGAAGCCCTACTGTGGAGGGAGGGAGTTTGGGGTGATAGCGAGTTCAGTGAGGGCCTTGGGGTGTGCAGAGAGTAGCTGGGCACAACTCTGCCCTCCTGGGGCTAGCATCCTCCCCAGGGAGACTCAGATGGTAAAGAATTTGCCTGTAATGCCGGATACCCGGGTTCAATCCCTGGGTGGGGAAGATGCCCTGGAGAAGGAAATGGCCACCCGCTCCAGTATTCTTGCCTGGAGAATCCCATGGACAGAGGAGCCTGGTAGGCTACAGTCCATAGGGTCACAAAGAGTCAGACATGACTAGGAGACTTCACTTTCACTTTCTTTGCCACGTGTGGGCACTGGCCTGGCTCTGGGGACACTGCAGTGGGCACCCTGCCCTCAGGAAACTAGGACCGGAGCCCCTCAGCCTTGAGGGGCCCGGATGACTCATACTGGGAGACCATGATCGCTGGGATGGCCCGGTCCATGCCATGCCATGGAGGTTGGGGGGATGGGCAGAGGGGGGCGCGCAATGGGCAGGGTCATGGTGGCAGCCTGAGCAGACACCCCTATGCTCGTAG
Seq C2 exon
CTTTTCCCCAAGAACTGGAATGGCCCCTCCACAGTGTGGATGTTTGCCCGGATGGTGCAGGCGCGGCACGTCCGGGTGTGGCCTTCTGATGGGCACCACCAGGCTGCCCCCAGCAGTGATGCCAACCTGGACGGCCCCCTGCGGGTGGAGCTGCTGGGCTGTGAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:49
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.324 A=NA C2=0.439
Domain overlap (PFAM):
C1:
PF0075420=F5_F8_type_C=FE(25.4=100)
A:
NA
C2:
PF0075420=F5_F8_type_C=PD(34.5=86.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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:
CATCATAGTGCAGGGGGCTG
R:
CTCACAGCCCAGCAGCTC
Band lengths:
274-1060
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]