BtaINT0130796 @ 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
chr3:14659269-14661048:-
Coord C1 exon
chr3:14660948-14661048
Coord A exon
chr3:14660573-14660947
Coord C2 exon
chr3:14659269-14660572
Length
375 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
CCCCTTTCCTTCCCCTACAGTTA
3' ss Score
11.16
Exon sequences
Seq C1 exon
GAAGTCCTGGAAACAGGACATGCAGCAAGGGAACCCAGAGTGGGCATGTGCCAGTGGCCCCATGGGCAGGAGTCTGGGGCCCAGGAGCCGCCCCCAAATCA
Seq A exon
GTGAGTGTGGGGCCAGAGGAGGTGCAGAGGCTAGAGAGGACTTCCAGCGGTGGGGACACTCCTGCATCAATTTCTCCCTTCGCATCTGCCTGGCTTGAGAACTGAATACCCAGAGTTGGGATGGATTTGAATGTCAGCTGTAGGGTGGAGGGATAGAAATTCTAAGCTGGGATTCAGGACTGGGGTTGAAATTGGTTCTGGTGTCAGAGCTGGAGTCAGATGAACTGGGGGTTAGTTTGGGGCCCAGACTGGAGACAGGAAAGGGGTCAGAGTTGAGTTTAGGACCTGAAATAGAAGTCGGAGACGGGAATGGGGCCCCAAATGTCGGGGCCTGCATTCTCCCCTTAACCTTTGGCCCCTTTCCTTCCCCTACAG
Seq C2 exon
TTAAAGAAGTCCTGGCTGTCCCCAACTCCATCCTGGAGCTCCCCTGTCCCCAGAGCTCGGCTCTGGCCTCTTACCACTGGAGTCACGGGGTAGAAGCCATCCCAGAGGCCCCTTCCACAGTCTACAATGGCTCCCTCTTGCTGCTTCTGCGAGATGGGGCGGGGGGTCTCTATCAGTGCTGGGCCACTGAGAATGACTTCTCGTACCCTGTGGTCTCCTACTGGGTGCACAGTCAGGACCAGCCCCTCGCCCTGGACCCCAAACTGGCGGGCATTCCCCGGGAGCGCATGGAGGCCCCGCTGACCAGGGTTGGCGGCGGGGCCGCCCTGGCTGCCCCGAAGTCCTACTGGCCCCACTTCCTCACCGTCACTGTGCTCCTTGCCCTGGTGCTCTCAGGAGCCCTCGTCACCTTCCTTGTATCCCCACTGGGGGCACTCCGAGCCCGGGGCAAAGTCCAAGGCTGTGGGACCCTGCCCTCCAGGGAGAAAGCCCCACTGAGCAGCGAGCAGTGCCTCCAACCCTCCAAGGAAGGCAGGACGTCTGCCAGTGACATGGACGCCGACAACAACCTCCAGGGCACAGAGGTGGCTTAAACTCTGGGTACAGGCTGGGGCTGTTGGATAGGGCAGGGCGTGTGGCCATTGGCTGGGGGAGCTGGGAGCTGTTCCTTTCTGACTAGGCTGGGAGTGGCACCGAAGACCGCTTTCCCCAACCAGAGGACCTTCTCTGCCATTCTGTGCCACTGATAGCACTCAGTGAGGCTGGGCACAGCAGAGCTGGCTCCCCTGTGGAACCTGCTTCTACCAAGCACGTGGCCTCTCTAAGCGGGGCTGCCCCAGACCTGGTCTAGGCCATGAAAGGAGGACCCAGAGAGGATCCTTCAGTTCTGGGCATCCTGGGACCGTCCAGAACATACCGCTGCAGGAGACCCTAAAACAACAAGCGCGTGAGCACACCACATCTGGAGACTCCACTCTGAAAGCAGCTGCCACCTTGGATACCAACACTCCCCTCTCCAAGGACTCTCCAGGACTCTGCAGGGAGCCGCTCCCTCCAGCTCACCTTATCAGCTCCACTGGGAGGTCTTTCCTGAAGTCTCACCTCCTTCCATCTTGCTTCAGTTGGGGCACATTTAATCTGTGCCCCTTCTGGCTTGGCTCGAATGGCAGGGGTAATCTGAGCCTTGATCACTCCTTTTCCCTGGCTGACCCCTGGACTCTCTTCTCTCCCCTCTCCTCTGTTTTGGAATTCAAAACCTGCTTGTCACAGACAGTTTATTTTTTATTAAAAAGACAAAGCTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.193
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(32.1=48.6)
A:
NA
C2:
NO
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:
TGGAAACAGGACATGCAGCAA
R:
GAGGGGCTGGTCCTGACTG
Band lengths:
342-717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]