BtaINT0130800 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012228 | SEMA4A
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:HGNC Symbol;Acc:HGNC:10729]
Coordinates
chr3:14674141-14675191:-
Coord C1 exon
chr3:14675086-14675191
Coord A exon
chr3:14674258-14675085
Coord C2 exon
chr3:14674141-14674257
Length
828 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCCTCCTCTCCTCACATTAGATG
3' ss Score
7.89
Exon sequences
Seq C1 exon
GAACTCCAAGATTCCAGACTGTTGCCCATCTCGGAGGACAGGGTTGTGGAGGGGAAAGGCCAAAGCCCCTTCGACCCCACCCATAAGCACACGGCTGTCATGGCAG
Seq A exon
GTGAGTATCGGTTTCCCTGGTCCATCCCAATAACTGCTTTCCCTGGTCACTCTGTGACACAGGGAATCTGACAATTTCCTGAAAGGCAAGAGGACAAAGGGAGGGGAAGCCAGGAGCCTCAGAGCATAAAATCAGAGGGAGTATCAGGTACCCCAACCAGATGAAGCTGCCACAAAGGAGGTGGGGCAAGATGGATGTGGAGGGATGCACAGAGATGGGAGGGTCCTGGAAGGGTCTCAGACAGGAAAGAGGCCTGAGAGTCACCTTCTGTTCAACAAGCAGACTCTGTATGAACAGCCACTCCGGTGTGCCAGGCATTGGGCTAGGAAACGTAGGGACTGCAAAGAGGAAATCATGGTGCTGTGCCCTCCTGGACACAAACCATCACTCCCCCCACCCCCTGGCTTCCTGAAGCCGGTGGCCTTTGACTGAGTGGGACCTTGAAAGACAGGTAGGTGGGCAGGGAAAGTGTTCCTGGAAGAAAAGGGTATGCCCTCATGTGTAGAAACAGAACAGCCATCCTGGAGAAACAATGAGTGATTCTAACTGGCGAGTGGTTCAGCTGGGTGTGGGAGGGAGGAGCCAGAGAAAGGCGGGGAAAGTGCCAAACACTGAAGGCCATAAAGTTGGCCAGTCCCTGTGGGAGGAGGACCTAAGAACAGTGCTCAGGGCGGGCTGTGAGCTGGGCTTTGGGACTCCACGGGAAGGTGTAGAACAAATAAAGAAGGCCAGAGAGTGATGTGAATGCTGACCCCAGTCAGAGGCAGATCTGAGAAGGGCAGGGGCACCCTCCAACTGACAAGGTCCCCCCTCCTCTCCTCACATTAG
Seq C2 exon
ATGGGATGCTCTATTCCGGCACCATGAACAACTTCCTGGGCAGTGAGCCCATCTTGTTGCGCACCCTGGGATCCCAGCCTGTCCTCAAGACTGACAATTTCCTCCGCTGGCTACAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.2=100)
A:
NA
C2:
PF0140314=Sema=FE(11.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACTCCAAGATTCCAGACTGTTGC
R:
GTTGTAGCCAGCGGAGGAAAT
Band lengths:
222-1050
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]