BtaINT0130793 @ 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
chr3:14663382-14665141:-
Coord C1 exon
chr3:14664961-14665141
Coord A exon
chr3:14663501-14664960
Coord C2 exon
chr3:14663382-14663500
Length
1460 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
TCAACTCTCTCTCTCCACAGGCA
3' ss Score
13.22
Exon sequences
Seq C1 exon
TGCTCCAAGGGCCCCTCCTCTGATAAAGCCTTGACCTTCATGAAGGACCATTTCCTGATGGATGAGCCAGTGGTGGGGACACCCCTGCTGGTGAAGTCTGGTGTAGAGTACACATGGCTTGCGGTGGAGACAGCCCAGGGCATCGACGGGCAGAGCCATCTGGTCATGTACCTGGGCACCA
Seq A exon
GTGAGTAGAGGGCTCCAGGGCACCCCTCAAGGGGCTGGAGCCAGGGTTGCAACTCAGGTTGAGGAGGGAGACCTTTGAGTCCATTCACTCATGCATTCACTCAACAAATTCTTTTTTTAATTGGATGATAATTGCTTTATAATATTGTGTTAGTTTCTTCTGTACCACAGTGTGAATCAGCTATACGTATACATATAACCCCTCCCTCTTGGACCTCCCACCATCCCACCCCTCTAGGTTATCACGAAGTAGCAAATGTTTATCAGAGCACCTGTGCTGTGCCTGGCACCCAGCTAGGCTCTGAAAATATAGCAGGGGAACCAAAGAGCCCCATCCCTAACTTTTCTGAACTTTCAGTCTGGTGAGGTAGAGAAGCATGAAGGGTTTTGGTGACCTTAGCAAGAGCTGTTTATCTTATTTATCTATCTTATGGGGGAAACCATGCTAGAAAGGTGATGTAAGGGAGGATAGAGGAGGGGTGTATAGACTTGGGGAGGGAGAAGATGGGCAGGAAGTAGAGGGAGCTCTTAGGCGAAGGCTTTTGTGTTTTCTATGAAGTAGGAGAACACAAGGTCATGAGTGGCGGGGACTGAGGGATGGAAAAGGCAGGTTTGAGAAGAGAGAAGTAGATTCAAATATTCTTTGTGGAAAGAAGGAGAGACGGTCTGTGGGGGGATGGGGAAGATTGCGAAGCATATGTATTGAGGGCCTGGCTAAGGTGGATGACCTTGAGCTTTAGTAGAAGAAGCCCGTCAGGTTCGTTCTTTCTTTTAGGACATCAGCTGTGCCTATATTGAGTACACAGACAAGAACAGAACAGACAAAAAGCTAGCTCCTTTTGGAGTGCATGGAGACAGACAATAAACATACTGAAGGAGTCAGTTACTTGGTACATTACGAGATCAGAAAATAAGTAGAACAGTGTGATGGGGTGGTCAGGAACGCTTGTTGGAAAGGTGGTAATTTGAAAAGGTGGTCGGGGTAGACCTTACTGAACTTTGAGTAGAGACCCTTGACGGTAGTGAGGGAGGCTGGTGATGTGATTTTCTCCAGAACTGATTAAAAGTCCACATATCCATGAAGAAAGGGGATAGTTTGGTTCCTCTAGGGCTGGAGTTTGATCAGGCAGTTTCCAAGGAAGGACTGAGAGGCAAGGGATTTCCAGCCATTTACGAGAGCTCCGTCTCCATGGCAACGGAAGGAAATGGTCTGACAGATCTGTGTCCAGTGCAGACTTCAGAAGGAACTTTCTTTCTTTCTTTTTTTTTGGCTTCAAGGCATGTGGGATCTTAGGTCCTCAAGCAGGGATCAAATCAGCACGCCTTGCATGGAAGCCCAAAGACCTAACCACTGGGCCACCAGAGAAGTCCCAGAAGGAACTTTCTGACAGCTGGGGAGGCCATCTGGAGTCAGAGAGCAAGCATGAGAGGCTAGGTGATTTCAACTCTCTCTCTCCACAG
Seq C2 exon
GCACAGGCTCCCTCCACAAGGCTGTGGTGAGTGGGGACCACAGTGCTTATCTGGTGGAGGAGATTCAGCTGTTCCCTGACCCTGAACCTGTTCGAAACCTGCAGCTGGCCCCTACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.044 A=NA C2=0.025
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(9.4=100)
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:
CAAGGGCCCCTCCTCTGATAA
R:
CTGGGTAGGGGCCAGCTG
Band lengths:
295-1755
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]