BtaINT0141448 @ bosTau6
Intron Retention
Gene
ENSBTAG00000008542 | SSPO
Description
SCO-spondin [Source:HGNC Symbol;Acc:HGNC:21998]
Coordinates
chr4:113460340-113461832:+
Coord C1 exon
chr4:113460340-113460403
Coord A exon
chr4:113460404-113461667
Coord C2 exon
chr4:113461668-113461832
Length
1264 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
CCTCCCTCCTGCACTCCTAGGCA
3' ss Score
8.59
Exon sequences
Seq C1 exon
GGTCTGGCAGAAGCAGAAGCTGACCACTGGCATCCTGGGCGGGGGTCACCCGTGCCCCCCACAG
Seq A exon
GTAATGTGCCCAAACTCCAGGCCGCCTTCCTGGCCACACCCCCCCGACCCCTGCCAGCCTTCCTGTTCTTTCAGGGCAGGGGGCTGTTACATCTCTGGAGTTCAGTTTTTTGACCCTTCTTGTCCTCTGACTGAGCAAGGGGGGCTCAGGGAGGCAGGTGTGGTCCCCGTGGACTCCTTGGCCAGGTCCAGCCCCTGCCCACCATCCTGGACTCCAGGGTACGAGGCTTCTGGCTGGTCCCTGGGGCTGAGCCTGTGCCCTGCAAGGGGTGGCTGCCTTCCCCAGGCCCCTGGCCCATCTGTGGGCTGCTGCCCAGAACTCCCTCTACCCCCCACCCCTGCACACACCCATTTCAGAAGCGTTTGCAGGCAGCAGATGTCTGTCAGTGGGCACGGGAAGCCAGGGTCACCCAGTTAGCGGGGTCCTAAATAGGACAAGGAAGGGGCTCCCGTTGTGTGCCAGCCCCCCCTGCAACCATGGCCACCTGGCCCTTCACCTGCACGAGGGCCCAGGAGAGCGAAGGTGGCCAGTGAGGGCTATCAGGGCAGCTGGGAATGACCTTCTCTCTTGGGACGTGTTGGGTCCATCTCACCACCTGCCCGGAGCCTCATTTTCCCCCTCTGTGAGCCCAGGAGCACTTATAATTGGTGCATATGGTCCCTTCCAGAAAGTTCTGAGTATAGCTATTCGGAAGCCTGGCTAGCAGTGCTTCTGCATCTCTTGTGAGAAGCCGCTTGAACCATCGCTTGGGTCCACAGAATGCAGACCCCCATGACGAAGGCTGCTCTCATCCCAAGTCTGGTTCTAGAAAAAAGGCTGTCTTTTTAAGCATGAATCTCTTGTACAAAATAGGTTCATCCCTCTTTTCCCTGTAGCTGCCAGGAGGCTCCTGGCCGATTTCTCTGTACCTGCAGTAAAGGGCTGGTGCTGAGTCTCTGGCCAGGCAGCTCCTCCTGCTGCCGTTTGTGTTTCTCCATAAACGTTGACTTTATGGTGAGTTTCACTTGGAGGCTGCTGTGTGTGTCTTTGTGAGTGGAGAGTACACATCTCACTCAAAACTCAGCTTTTCTTCTGCATTCAGTTAAAACCCTTCTTGTGCCCCTGGGACGACCGAGTCCCTTTTCCATTTTGATCTGAAGCCCCTCAGAAGGTGGGGTGTCACCTGTCACCACCCCAAGACCTGGAAAACCCTCTGGAGGGCCCGCGTCGGCCTTATCTCAGGGACAGGGAACTGATGGGCTCCCCCTCCCTCCTGCACTCCTAG
Seq C2 exon
GCAAGGGGCCAGCGAGTCTTGGGTCCGAGCCTCACCCAAGTCCTGGGGGATCTGTGCAGACTGTGACCCCCACCTCCCAACCGGAGGCACAGGCCCTGAGACCGGAAATGGCAGCTGTGACGGTGCTCCCCCCACACCCCATGGTGACGCCCGAGGTTCCTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000008542:ENSBTAT00000043975:53
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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:
GGTCTGGCAGAAGCAGAAGC
R:
GAACCTCGGGCGTCACCAT
Band lengths:
223-1487
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]