BtaINT0130823 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021920 | SEMA4C
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:HGNC Symbol;Acc:HGNC:10731]
Coordinates
chr11:2784990-2786017:-
Coord C1 exon
chr11:2785947-2786017
Coord A exon
chr11:2785820-2785946
Coord C2 exon
chr11:2784990-2785819
Length
127 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CATTTTCTCTGCTGCTACAGTCA
3' ss Score
5.56
Exon sequences
Seq C1 exon
GTCCCTGCTGATCCAGCACGTGACGGTCTCGGATACCTCAAGCATCTGTAATTTCCGGGGCAGTAAGAAAG
Seq A exon
GTGAGCTGTTGTCTTAGTCCTCCTTGTAGGGTGTACGGGCCTCGGGGGACCAGAACCGGGGTGTCATTGTCCCCCCTTGGCCTGGGCGTCTTGCACCCACTGACTCTCATTTTCTCTGCTGCTACAG
Seq C2 exon
TCAGGCTCACACCCAAAAACATCACGGTGGTGGCAGGCACAGACCTGGTGCTGCCCTGCCGTCTCTCCTCCAACCTCGCCCACGCCCGCTGGACCTTCGGGGGCCGTGACCTGCCCGCGGAGCAGCCTGGCTCCTTCCTCTACGATGCCCGGCTGCAGGCCCTGGTGGTGATGGCTGCCCAACCCCGCCACGCCGGCGCCTACCACTGCTTCTCGGAGGAGCAGGGGGCCCGGCTGGCTGCCGAGGGCTACCTCGTGGCGGTGGTGGCGGGCCCATCGGTGACGCTGGAGGCCCGGGCCCCGCTGGAGAACCTGGGGCTGGTGTGGCTGGCTGTGGTGGCCCTGGGCGCCGTGTGCCTGGTGCTGCTGCTGCTGGTTCTGTCCCTGCGCCGGCGGCTGCGCGAGGAGCTGGAGAAAGGTGCCAAGGCGGCCGAGAGGACCCTGGTGTACCCGCTGGAGCTGCCCAAGGAGCCCACCAGCACCCCCTTCCGGCCTGGCCCTGAGACAGACGAGAAGCTCTGGGACCCTGTGGGCTACTACTACTCAGATGGCTCTCTCAAGATCGTGCCTGGCCACGCCCGGTGCCAGCCCGGCGGTGGGCCCCCCTCGCCGCCCCCCGGCATCCCCGGCCAGCCCCTGCCTTCTCCGACACGGCTCCACCTGGGAGGTGGCCGGAACTCCAATGCCAATGGCTACGTGCGTCTCCAGCTGGGAGGGGAGGACCGCGGCGGCCTCGGGCATCCTCTGCCCGAGCTTGCCGACGAACTGAGGCGTAAACTGCAGCAGCGCCAGCCGCTGCCGGACTCCAACCCCGAGGAGTCCTCAGTATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021920:ENSBTAT00000029225:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.380
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(37.9=88.0),PF138951=Ig_2=PU(1.3=4.0)
A:
NA
C2:
PF138951=Ig_2=PD(97.4=27.1)
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:
GCATCTGTAATTTCCGGGGCA
R:
TCCTCCGAGAAGCAGTGGTAG
Band lengths:
250-377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development