BtaINT0130804 @ 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
chr3:14664961-14671896:-
Coord C1 exon
chr3:14671746-14671896
Coord A exon
chr3:14665142-14671745
Coord C2 exon
chr3:14664961-14665141
Length
6604 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
CTGCCTCCTTCCCCCTTCAGTGC
3' ss Score
11.62
Exon sequences
Seq C1 exon
GCACGTTGGTGGGACCAGGAGCTCTGCTGTCTGTGCTTTCTCACTCAAGGACATCAAGAGTGTCTTTGAGGGGAAGTATAAGGAATTGGACAAAGAGACTTCACGCTGGACTACTTATGAATATCCTGATATCAGTCCACGGCCAGGCAGT
Seq A exon
GTGAGTATTATCCATGCCACTGAGTAAAGCCCGCCTCCCCCAGACATATATGTGTCAAAGCACCTCTCACAGCGTGATAGTGCCCCATAAATGCTAGTGCTCCCCACACCCCCAAGTCCTGTCTGCTCAGATATTCACCATTCCAGCTGCCCACGTTCCACATCCATGGTGTCCAGCCCCATCCTAAATACAGAACAGCACTCCTGCACCCCAGCTAAGTGCACACGATATGCTTGGGTATATCACTGAAAAAACAAGGGAGCACAGGCTGTGCCAGGGACTTTCCTGGGCCTCTTCATCTGCATTTCTTATTTAACTTTTGTTTTTGGATCGGAGTTGTATATGTACACCATTTGAAGGAGATTTACATGGTTGGTTACAAACAGCAGCCCAGTTTCCTCTCTCCAGCACTTTTCCCTCTCTAGAGACAATCTCCTTCAACTCTTTTAGCTGATTCTTTTGATTTTATCTCCAAATCTCAAAATACGTTTATTCCTATTCCTTGCTGCTTCCATTTCAGGCAGCAGCTATTGAATTCCCATTGTGGATGGTGAAGATTTAACCGTGTCTCCCCATCCCCACCCCCCACTCAGCGATGAGCTGGAGCTGACTTGCAGCAACTAGCAAGAACCCTTTGTGCATCTCTTTCCAAATCCGAGTTCAGTGACATTACGTTGATAGCTTGAAATTAACCATGGTGGGAATAATACATTATGGAAATCAGCAAACACTTTAAATCATCACCCCAGAGCAGCCTTACCAGCACACTGCTGTACCCACCTCTTATCTCCCAGCATTGGTTTATAGTCAGTTTGGTCAGGCCAGTATTTATATTATGATTCATTACTCACAACTGAGCCATATAGTAGGCCATGATTATTTTTCCTTTTTGCATAATTAAAAAAATTTTCCCTGGGGTTAGTAATTATCTTGATTTTTTTTTTCTTGCTTTGTTTTCTAAGCTCTTATCTTTATTTCAACCCCAAACTCTACCTCAATTAACTGAATCTCTTTTGAAAACAGACCCATTTGGTAGTCTAAGAATTTCATTTTCCTGGAAATCCTTTCTATCTGCTGCAGTCTTGACTACATCTTCATCTCATGTACATCCGGAGCACAGCTGCCATCCTGGAAGCTCCCTTCCTCATCATTCTGGGCATTCCCTTTGCCTCTTTCTTGTGATAATCTGGTGTTTCTTGCATCCCACAACTTCCTATTTTTTCTTTCTTTCACTGTCTTATTTTAGTGGAGGATGGGTGGGTGGGTGCTAAGTTGCTTCAGTTGTGTCCGACTCTGTGCGACCCTATGGACTATAGCCTGCCAGGCTCCTCTGTCCATGGGATTCTCCAGGCAAGAATACTGAGTGGGTTGCCACGTCTTCCTCCAGGGAATCTTCCCAACCCAGAGATCAAAACCGTGTCTGTTATGTCTCAATACATTGGCAGGTGGGTTCTTTACCACTAGAGCCACCAGGATGGCCTCTGTAAATTCCTGGAAAAGAATACACAGCAGGTAAATTTTTTTGAGACCCTGAATGTCTGAAAATGTCTTCATTCTACATTCACCTTTGATAGTTTGCCTGGTTGTATCTATTTTAATTCTAGGAAAAAATAATCTTCCTTTCAGACTTGGAAGGCATCCTCTATTATATTCTAGCTTACAGTGCTACTGTTTGAGAAGTCTGAAGCTATTCTGATCCCCAAAGCTTTGAATATCTGTTTTTCCCTCTGGAATCTTGTCGTACCTTTTTTGTGTTGCTGGTTATTTTTTTGTTGTTGTTGCTGGTTATTTTGAAATTTCATGATATTGTGCCTTGATGGGATCTTGTTCATTCATGGTCCGAGTGTTCACTTTGCCCCTTAGGCCTGGAAATTTAGTTCTTTCAGTTCTAAGAACTGAAAAGAACTGTTAACCTGTTGCTTGAACTGTTACCTTTTCATTTAATACATATTTTTTAAGGTCACCTGTCACTGTTGTAGGCAATGAAGACATAGTAGTGAAGAAAACAAAAATCTCTTTTTTCATGGAGAGAATATTCTACTGTTGGGATGTTTTCTCATTTCTTTCTGAACCCCCTGGATTGGTTGGTCCTATAACTTTTAAAATCCTTTTTAGGAATTTTCCCAAGTCTTTGGTTTTGTTCTACTTGCTAAGAGAGTATCTCAATTTTTTTATCTTCTGATCCTTCTGTCAGATTTTAAATTTCTGCTAACATATTTAATTTCCTAGATTTTTTGAGCTTTGTATATGTCTTATAAATACGTTCTATTATGGAGAATTTTAAACATATAAAAAGTGGACAGAATAGTATACTGCTGCTGCTACTAAGTCGCTTCAGTTGTGTCTGACTCTTAGCGACCCCATGGACTGCAGCCTACCAGGCTCCTCCGTCCCTGGGATTCTCCAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGAACGGGGGAGCCTGGTGGGCTGCCATCTATGGGGTTGCACAGAGTCGGACATGACTGAAGTTACTTAGCAGCATACACCCATCAGCCAGCTGCAACTCCTCGCCAGTCAGACCACTTCATCTCTACTCCACTCCCTTCCCCTCTTATTTTCTGAAGCAAATTCTGGGCATCATTTCATCTGTGTTAGTTTCCTATGGCTGCCATAACAAATTACCACAAACTTGGTGGTGTAAAACACCAAGAACACCAAGAAATTTATTCCTTTACAATTCTGGAGGCCAGGTGTTTGAAATCAAAGTTGCAGTCAAGGTTGGCTCCTCCTGGAGGCCCTGAGAGAGAATCCATTCTGGGCCTCACTCCTGCCTTGGCTGCTGGCAGGCTTTGGTGTTCTCTGGCTTGTAGGCACCTCACTCCCGTCTCTGCCTCTGCCGTCACGTAGCCTTATCTCTGTGTGTCTCCTCCTCTTCTCTTATGAGCACACTTGTCGTTCGATTTAGAGCCCATTGTGATCCAGAATGAGTCATCTTGAGATTTTTAAATTATGTCTACAAATAGCCTTTCTCCAAATAAAGTCACACTCCCAGGTTTTCAGTGGGCATACCTTTGGGTGGCTACCATTCATCCCATTACTTCATCCATAATGGTTTTAGTATGTATCACCAAAGATAAGGGCTTTGAAAAAAATAATGTATAGTTCCATTATTACACCAAAAAAATAATGCATGCGTGCATGTTTAGTTACTCAGATGTATCTGACTTTTTGTGATCCCATGGACTGTAGCCCGCTAGGCTCCTTGGGATTTTCCAGGCAAGAATACTGGAGTGGGTTTCCACTCCCTTCTCCAGGGATTGAACCCAAGTTTCCTGCATTGCAGGTGGATTCTTTACCATCTGAGCCACCAGGGAAGCCCCCTACCCCGCCTAAATTAATAATAGTTTCTTAACCTAATATGCAAAAGTATTCAAATTTCTAATAGTCTCATAGATATCATAAGGTTTTTTTTTTTTTAATATAGTTTGTTTTTGAAATCAAAATCAAAATAAGATCTGTAAGTTTGGATTGGTTGTTCTTTTCAGTCTCTCTTAGTCTGTATGTTCCCTTTCCAACTTCTTTCTTTCTCTTACAATTTATTCGTTATATAGGATTTCCCACAGTCTGGATCTTGATGATTTTGCATTGCTGTGGTGGAGTTTTAAGTATTTTCTATAAATTGGTGTTTGGATCTAGAAACGTGATCATGAAAACTTGCTCTTAAAGTTTGACTTTGGGGAGCAAAATAAAAACTTGTATTAGTTTGGTCTTCTTTCAGGACATTTATAATCTCTGGCTGCATTCGTTGGAATAAGAACTCCTCTTTTGAAGCATTATGTATGTTCTTGTTTCATGGGTATGCTATTTTCATACTTCTCTCTCTTAAGGTAATAATGATACTTCGCTGTGAAGTTTTCTTTTCTCTGAATCATTTGTTTCCTCTTAAAGTTTATTAATTTTTTTCCGTGTCTCTGTTTTTTATATCTTTCATGTCTGTGGTTTCACTCACATATTTGGTCATCCTTGGCTATCTACTCATAGTTATGAGGGAGGGGGCCTTGAAGCTGTGGAAACTCTGCACCCTGGGTATGACTTGGCAACTTGAACTCCATGATAACTCCACTGTGAATGGGCTGGCTAGGCTGCTTTACTGGAGACCTTCAATATCAGTATCTTTAAGTCTTTTCTTTTGGGCCTTTAGTCAGCTTTCCTGGAGCAGATTCTTCTAGTCTTGTCTTGGAGTAAGGCGGTCTGGCTCCTGGGATCTGGGAGTCATGGGGAAGAAAGGCTGGGGGTGGGGGAAGAGTCTCAGCAGGTGCTGTGTCTACCTGCATTTAATCCCCTGCCTTCATCATGGTGTGTCACCTCTCTGCTGTCCTCCAACCAGAGTCCCTCTGCCTTATCCTCTCTAGAGAATAAACCTCCAGTCCTGGGCCAGGGTATGGAAGGGACAGTTACTCAGCTGCATGGAGCTGGGAAGAAGTCTGCCTGCTTCTTAAATAGATTTTCAAATATAGCCTTTCTTTTGCCCCGTTTCCAGAGGGGACTGAGGCCACTGATTTATGAACTTCAGAAATTCTACCTTATAAATAAAAATTTAAGCCTGGGCTGGCTTAGAAAGACTCTTTTTTCCTGCTTAGTCTTTTCCCTTTTGTTCATTTGCTTTCCAGCTTCCCAAATGTGGCTGCTTTTAACTCCTCTCATGTTCTCATATGTCTTTAAAAAAAAAAAATCCCTTTGGGAGGAAGCGAGAGTAGGTACATGTGCTCATTCTGGCATCTAAATGAGATACAGATGTTATCGCGTCACTTTACAGATAGGAATTTTCAACTCATAGAGGTAGGGTAACTTGTCTGAGGACACAGCATGAGGTGATGCAGTTGTGGCTGGCTTTAAGACAGTGCTGTTGGAAACGGAGGACAAGAATCGTGACCATTGATCAGGACACAGGTGTCCCAGAGCTGCAGTATGCTGTTGTTGGCAGGGCCTTTGGAGAACAGCCGGTCCAACCCCCTCATTTTATGGGTAAGAAAAAGAAGGCCCAGAATGGAGAAGGGACTCTCCCCGAGTCGTGCATCCAATTCATGCCAAACCATGATGCAAAATACTCCCTGCTACACCACCCCTTTTTGTGACAGACTGCATTCCATTATTGACTCTGTGAACATTTATTGGGCCCCAACTGAGTACTAGGTCCTATGCTAAGCCTGGGCCTACAGACATGAGTTCAGGGTGGTCCTTGCCTGCAGGGGATCCTCACCCTACATTCTGCTGGTGGCCGGGCATCCTTGGTGACGGGGATGATGGGTAGAAATAATGACAGCTAAAGCTTATCAAGTACTTACTTCATGCCAAGTACTGTTCTAATTACTTTTCATGTAAGTCACTTGCATCCTCATAGCAAGTCTGTGCTGTGTTGGTAATAGGCCCATTTCACTGTTAAGGAACCTCAGACATGCTGAATTCAGACGCTGCATTTTAAAGCCAGGCAGTTCCAGAGTCCAGCTTTAATCCCAATCCTGAAATGAAGACTGCCAAGAGGGAGGGAGGCAAAGGAGATTAGCCAAAGGGGAGGGAGGGAGAGAAGAGGCCACAGGTGGGTTGAAGGAAAGGAGAAAGCTGACCTGATCTGCCTCCTTCCCCCTTCAG
Seq C2 exon
TGCTCCAAGGGCCCCTCCTCTGATAAAGCCTTGACCTTCATGAAGGACCATTTCCTGATGGATGAGCCAGTGGTGGGGACACCCCTGCTGGTGAAGTCTGGTGTAGAGTACACATGGCTTGCGGTGGAGACAGCCCAGGGCATCGACGGGCAGAGCCATCTGGTCATGTACCTGGGCACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.059 A=NA C2=0.044
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(14.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]