BtaINT0130838 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001941 | SEMA4D
Description
Bos taurus sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (SEMA4D), mRNA. [Source:RefSeq mRNA;Acc:NM_001098160]
Coordinates
chr8:90246216-90249925:+
Coord C1 exon
chr8:90246216-90246259
Coord A exon
chr8:90246260-90249715
Coord C2 exon
chr8:90249716-90249925
Length
3456 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TTCTGTCCTCTGTCTCGCAGCCT
3' ss Score
9.79
Exon sequences
Seq C1 exon
GGGACTGATTCAGGAAATGAATGGGGACGCATCCACTTGCCCTG
Seq A exon
GTAAGTTGCCCGTCCCCGCCACCTCCCCTTTAGGGGCAGCCGGGTCTCCTAACCATTTCATGACGCTTTGCTGTTGTAGCATTTCGCACGTTTTGTTTTTCTTTCTTTACTCGGAACAGAGGTCGAGTATCTCGTGGCAGACCCCTGTGATGTTTCTTTGTCCCTTGTATTGCAAAACAGGATGCCGAAGCCATGCAGAGTGTGTTTACTGGAAGGCACTCTCATCCCAAACCGTGACGTCCACTCTTGATATGCCTCTCTCTTCCGCTTAGCTTGGGGCCACACCTCTTGTGGGGCTTCCCAGGTGGCTCAGTGGATAAAGAATCCACCTGCAATGCAGGAGATGCAGGAGACATGGGTTTGATCCCTGAGTCGGGAAGATCCCCTGGAGGAGGGCATGGCAACCTACTCCAGTATTCTTGCCTGGGGAATCCCATGGACAGAGGAGCCTGGCAGAGGAGCCTGGGGGTCACAAAGAGTCGGGCGCAACTGAGCAACTGAGCATACATGCATACACACTTCTTGTGAGCCGGAGGGAGGTGCTCAGGAGAGATTAGTTCGCGTTCCCATCCCACCCCTGCCAGGAGATCAGGCATGTTCCAGCTGAAGGCAGGTGTGCCCTGGGCTCCCATCCCTAACCTGACAGATGTCATCAGTTAAGACAGGTTTAGGAGGAGGGGGCAAGGCCCACCGAGCTGCTAGCAGAAGTTTGATACCTTTGACTTGGCGCCGCCACCAGAAGGCACAGCTGGCTGCTGTGCAGCCTGCCTGGCCTGGGAGTTCTCCCCGTCCCCCAGGGCTGCCACTGGGAGCTCATCTTTGCTTTTTGGTCATGCATGTCTTTATCTCCTTAGCTGTTCTGGAAGATTCCATGTTGCTCCACTGGGTGAAATTCTTGTGTCCTCTTGTACGTGTTGACCTATTTTTGAGAGAAGTATTGAGCAGGGTTGTTGATGCTGTGCACATTTATTTTAATGTTCCAGATAAAATTAAAGAAAGTTACCTGCAGCATTTTTTCAAGCATGGCGGCACAGCAGAACTCAAATGTTCCCAAAAGTCCAACCTGGCCCGGGTGGTATGGAAGTTCCAGAACGGCGTGCTCAAGGCCGAAAGCCCCAAGTACAGCTTGGTAGGCAGAAAGAACCTGCTCATCTTCAACCTGTCGGAAGGAGACAGCGGGGTGTATCAGTGCCTGTCGGAGGAGAAGGTCAAGAACAAGACGATCTTGCAGGTGGTGGCCAAGCATGTTCTGGAGGTCAAGACGGTCCAGCGAACCACAGTGGCCTCTACCTCTCCAGCCACACGGACAGAAGGCAGTCGGATCACCCCCAGAGTGTCAGTGGGGCCCACCCCAGTCTCCTTTCCTCAGACCCCAGCCGTGCAGGTCACCACGCTGGGTGCTGTTCCCCCACCATCCAGCCCCGTGGCACCCACTAGTACGTCCTGCGAACCAAAGATCGTCATCAACACGGTCCCGCAAGTCCACTCGGAGAAGACATTGTATCTAAAGTCCAGTGACAACCGCCTCCTCATGTTTCTCTTCCTCTTCTTCTTCGCCCTCTTCCTCTGCCTCGTCTCCTACAACTGCTATAAGGGCTACCTGCCCGGACAGTGCTTGAAATTCCGCTCGGCCATGCTCCTCGGGAAGAAGAAGCCCACGTCGGACTTCTCAGACTTTGAGCAGAGTGTGAAGGAGACGCTGGTGGAGCAGGGCAGCTTCTCCCAGCAGAATGGGGGACAGCCCAAGCCAGCCCTGGACACCGGCTACGAGACAGAGCAGGACACGATGGCCAGCCGGCTGCCCACTGACCGGGAGGACTCGCAGAAGATCGACGAGCTCCCGGTCAGGGACCGGCCGTTCGACGTCAAGTGCGAGCTGAAGTTCGCCGACTCGGATGCGGACGGGGACTGAGGCTCCGGCCGCCCGCAGGGTCTCTGTGTTGCCAGTTCAGTGCTCCATCCAGTGCTGCGTAGGTAGCCGTCGTCAGCAAACCTCAGCCTTCTGTGTCTTTTTTCTTGGGTCGCACTTGTGACTTGGTTTCTCTTTGTCCTTTTGGAAAACAGCAAGCATCGAGTCTGGCCTCCCTGGTCGGTGGCGCGTTTGGAGTCGCACCCGCAGGCTCACCCACGGCCGCTCTGCGGCGGAAAGATGGCCAGACTGCCACTGGTCTGAGAAGAAGGGCCATGAACGTCCCCTCCTCGTAGCAGCCACTGAAAGATAATTTAATTCCAGATTGGAAATGACGTTTTAGTTTATCAGATTGGTAACTTATCACCTGTTGTCCAGGTTGGCACGGACCTTTCCTTCCACGTCATTACTTTTTAGGATTTTGCTTTAATTATGTTGGCGTGTTGGGTCATTTTATTTTTTTAATTACTAAAGCAGATGTTTTAATATTTGGAAGATGTACATCTTCTGAATTTTGTTGTATATTAGGATAAAGGTATGGCTTACGTTGCTTAAGATTCTCAGGGATAAACTTACTTTTGCTAAATGCATTCTTTTCCGCTTTTAGAAATGTAGACAAAAATCATCTCTTGATCACACTTCTTTTTTTAATTATTCTTAAAATTTTGTTCCTTGAGGGAAGCATCATTTTCAGAGATTTTTCTTTCTGTACCTTTTTACTCTTGTCTTAACTCTTTCGAGGAGAAGGCTATGGAGGACCATTCCACGACACTGGGTAGAGTTTGGAGGGAGGGACGGGCCCCAGACTGCTATGGATGGAGCTGGGCTAGCCCAGAGCTGAGAGGACAAGCGTGTTACAATCTAATGCCCATGGCCACTGGTGAAAACCTCTTGTTCAGGCAGAATGTTCTCCAGGATGTCTTGGTCATCTGAACATCTCCTTTTCCATTTTGCTTCCATCTCATGCTCTCTGCCTGCCCAGACTCTCTGGCCTAATTGAGCTGTCTACAACTGGAAAAGAGCTGGGTGGCCAGGGGGCAGCCAGGCCAGTGACCACAGCCCCCCAGCCCCCACATGCTGCTGCCGCAGACCTGCCAAGCCTGGCGCCATCTGTCAAGGTGCAAGTGGGCCGCACGGTCCTATCATCACCGACATCACACTCCACCTCCTGCTTTCCAGACGCCCACAAGAGGAGGCTTTCTTTCCGTGGCAAAGAGCAATAAACTCTGAGCGTGTGTGCCTGTGTGGCCGATGTCATCTTCCAGCATGATAGGATTTGACCGTTCTGGTGTAAACATTTGTGTTTTATAAGATTTACTTTGTTTTTATTTTTCTACTTTGAATTGTATACATTTGGAAAGTAACCGAATAAACAGAAGCTTATATCCTTGATGCGGGGACGTGGTTCTCTGCGGCTCCTCTGCTGCCTCCCCACGTGGCCTGGGCCCCTTTTCTCTCCTGTGCTTCATTCTCCTTCCCTGGCATGCGGTGCACTCCTGATGACTTCTCCTCAGAGCCCTCTCTCTTTTCTGTCCTCTGTCTCGCAG
Seq C2 exon
CCTCATCTCCTCTGCCCTTCCCTCCTCCGGGGTCCTCTTCCCTGTCCTGTCTGGGCCCCGACTCATCTTCCTCTCCCCGAAGCCCCTGGCCGGCCTCGGGCCCAGGGCCTGACCGCCGCCTGCAGGTCACCTTGCTGCCGCCCTTCCTCAGCGACCAGGCCCAGCACGTGCATGCCCTGGGGACCTTCCATCTCTTCTGCCAGGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001941:ENSBTAT00000002525:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.394
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(26.4=87.5)
A:
NA
C2:
PF138951=Ig_2=PU(26.4=33.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]