BtaINT0130795 @ 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
chr3:14660948-14663272:-
Coord C1 exon
chr3:14663115-14663272
Coord A exon
chr3:14661049-14663114
Coord C2 exon
chr3:14660948-14661048
Length
2066 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TTTTTGCTTTCTCTCCTCAGGAA
3' ss Score
12.5
Exon sequences
Seq C1 exon
GGAGCAGTGTTTGTAGGCTTCTCAGGAGGCATCTGGAAGGTTCCTCGAGCCAACTGTAGTGTCTACGAGAGCTGTATGGACTGTGTCCTTGCCCGGGACCCTCACTGTGCCTGGGACCCTGAGTCTCAAACCTGCCGCCTCCTGCCCACCCCCATCCT
Seq A exon
GTGAGTGCCAGTTACCCTGTATGTGCTTCTGGGCTCCTTCTTTCCAGGTGCTGTGAGGTTGGTGCAAAAGTAATTGCGGTTTGGGGCTGTGAATTTTATATCATTTTAACTAGGCTCGAACACATCTTTATTAATCAAAATAGGAACTGTTACAATTAATACATTTTTTGCCAACAAGAAATAAGTTGCTTTATTCCCGTAGCATAAAAATCTGTGCTTCAGGATTCGATGAACTCTTGGAAACCATTTTCTGCTGTTTGTGGAAGCGTTTTCCCTTCAAAAAGTTGCTTGAAGAAGTGGTAGTTGGTTGGCAAGAAGTCAGGCAAACATGGTGGATTTGGCAAAACTTTGCAGCCCAGTCCGTTCAGCTTTTGAAGTGTTGGTTGCGTGGCATGTGTTTGAGTGTTGTTGTGGAGAAGGGGCCCTTTTTTTTGAACTGGCTGCAGGCATTGCACTTTTCAGTTCATCCCATTGACTTGCTGAGCAAACTTCTCAGATGTCATGGTTTCGCCAGGGTTCAGAAAGTTGTAGTGGATCAGACATTTAGTGGTTGGACCAAAAAGAAGCTCGAAAGCACTTCCCAAAGCCACACTTGCACCAAAAAAGGTCCTGACCAAACGATGAGGAAGAGAGCCCTGGGAGGCTTAAGAGTAGCATAAGGAATTCTTTTGCCACTAACTCCTCAGAAGCTGGAAGCAGCCAGCCTCCAGGCACCAATTTAGGTCCCTGTCCGGAGTCTGAGGAGTGGGGACTAGGAAGGGCAATTCAGAGTTGCTGTAGGGAATGGGGAAGGCAGGCCCAGGGCTTCCGTCGGCCTGATACCATCGGACCACCAGAGGGCGCTCCAGTCCTCAGCAAGGGAGGATGATGGGGCCTTCATGCTCCAGCATCCTCTACCTAAAAAAGTGGAAGTCCTTCCTGCAGCCTAATGGCCTTCCTGCCTGCTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAAAAAGAAGCTCGAAAGCACTTCCCAAAGCCACACTTGCACCAAAAAAGGTCCTGACCAAACGATGACCATGACCTCTTCTTGGTGCAGGTTCGGCTCTGGGAAGTGCTTTGGAGCTTCTTCTTGGTCCAACCACTGAGCTGGTAGTCTCTGGTTATAGTATACAATCCACTTTTCTTTTCTCATCACACATCACAATCTGATCGAGAAACGGTTTCTTGTTGTGGCTTAAAATAAGAGAAGACAACACTTCAAAATGACAATTTTTTTGCTTTGTGGCCAGCGCATGAGGCATTCACTTATTGAGCTTTTTCATCTTTCCAATTTGCTTCAGATGCTCAATGACCACAGAATGGTCGACATTGAGTTCTTTGGCAGCTTTTTGTGTAATAGTAAGAGGATCATCTTCAATGACCTCTCCACTGGTCGTTGTCAGCTTTCAGTGGCCGGCCATCACACTCCTCATCTGCAAGGCTCTTGTCTCCTTTACAAAACTTCTTGAACCACCACTGCACTGTACGTTTGCTAGCAATTCCTGAGCCAAATGCATTGCTGATGTTTCGAGTTGTCTCTGCCGTTTTACGACCCATTTTGAACTTGAGTAAGAAAATTGCTCATATTTGCTTTTTGTCTAATATTATTTCCATAGTCCAAAATAAATATAAAATAAACATCAAGTAGTAGGTCATTAGCAAAAAACATAAAGCAAAAAATATACATTAAAATGATGTATAACATAACCACATTTATTGAGAATGTATTCCAATATCAAATGGCAAATTTCAACAATGCAAAAATCGTAATTACGTTTTCATCAACCTAATACTAACACATCGCCTCCAAGACAACCCCCAGCCTCTGGGGGCTCCTCCAGGGATGGAGTTATACCCGGCATTGTTGAGCTGTTTCAGCCCACCCTGGGCTTCTCTTCCCCTGATCTCTGTTCTACCTTGTCACCCCGACCCATCTTTCTCCCCACTGCACTTCCCTCTCTTGCTCCCTCCTCTTCCCACTCTTGCCTGTTTCAAGGGATAATTTTTGCTTTCTCTCCTCAG
Seq C2 exon
GAAGTCCTGGAAACAGGACATGCAGCAAGGGAACCCAGAGTGGGCATGTGCCAGTGGCCCCATGGGCAGGAGTCTGGGGCCCAGGAGCCGCCCCCAAATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0143720=PSI=PU(66.0=66.0)
A:
NA
C2:
PF0143720=PSI=PD(32.1=48.6)
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]