BtaINT0130792 @ 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
chr3:14677154-14679216:-
Coord C1 exon
chr3:14679058-14679216
Coord A exon
chr3:14677315-14679057
Coord C2 exon
chr3:14677154-14677314
Length
1743 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTCTCACCACCTCTCAACAGGGG
3' ss Score
8.16
Exon sequences
Seq C1 exon
ACAGCCCCTGGCTGAGCATGGCCCTTCCAGCCCTGGGCCTGGACTCCTGGAGCTTCCTGGGCCTTTTCCTCTTCCAGCTGCTCCTGCTGTTCCTGCCACCGGCGACAACTGCAGGGCGTGAAGGGCAGGGACCCACACCCAGGGTCAAATACCATGCAG
Seq A exon
GTAAGGATCTGACAGTCAGGAAGTAGGGGATGGCAGCCCCGGGCTGGAGGGGGTGGAGGAAGGAAAGAGAGAATGGAAGGAAAGGGGTAGGAAATTGGACTTGGAGAAACCACACTAGATAAGTCATGGAGAGGCAGAGGGCGTCAGGGAGAGAGAGACAGCCAGAAATAGAAATTCAGGCTGAGAAAGGAGTGAATGATGAAACTCACTTGGGGGAGAGACTGAGGAAAGGGAGGTGAGGAGAGCAGGGGGCCAGGGGCGTTGTGCCTTCTGGTTCTCCAGAGCTGGTGATTTCTCTTTCCCTCCTTCAGTGTCACTGTTATCAAACTGGGCACTTCAAACCCATAACTGCTTTCATGCCCCTAGGACATTTGAGGCTTAAGGGAATCCGTGGACCTGGTGACCCAGGACACGCAAGTGCACAGATGATGCTGGACCACGCTGTGTCCAATACTGTGGACACCAGGAATACAAGAACCCAGAGTAGCCTGGCTGGTATCTGGGCCCTGGGACCCTGTAGGCACAGCTTGACTGGTTTCTTACTGAGGCTGTGGGGGCTGCTGGCCTTCCACCTGCAGGGAAAAGACTCAGGAAAGGACATGGGCCCTGTCGGAGTTGCAGGGGCAGGGTCTCCTGGGCATGGCTGAGTCTTTTGCATCTTTCTGGGGCAACATGGTAAAGGAAATGCATGTTGCCCATTGATGGAAGGGCCTCCCTTGTGTTAGGTGCTGGGATTACAAGCATAAACCCTGCCCCCAAGGTGCTGATGGTCCCCAGGGGCAGGCAGGTGGGCTGTCACACAACCATACTTGAGGGTGATCAGTTCAGTGACAGAGGGGTTTATACAGCTCTGGGGAGGCCAGCCTCTCTGGCACCTTGCCACATGTTTCCCCAACTCCTCTTCGTGGTTGGTACTAAGATTCTCTGAGCCTCCAGAGCTAACAGTTAGCTCATCAGTCCTCTAATGCGAAAGTGCAAACGTGCTCATGAGAGAGAGAGTTTGAGAAGCTCATCTCTCCTCGCTGATGTGCCAGGGGCCCTATGTGCCAGGGGAACGGGCACACACGCCCACCTCCGCCACATCACAGTGATGGGGAGACCTCAGGGAATCTCCCACAGCCAGCCGAAATCCCCAGTCTGGGTGATATACAGGCGCCTGCAGGAAACTCAGGAGAAAAACATTTTCTTTCTGTTCCACCTATGGCAGTGGTTCTCATGGTAGAAATTTCCTGTAGAGGAGGGAAGGAAAGTGGGGTTGGTGAGTGGGACCCCTGAAACCCACAGTTACTCTGACACATAGTCCTATCTACCTCTAGCCTTCTTGTCTGTGGGTGCCAACACCTTCCTGTCTGTCTATCTGCTCTCTGCCCTCCCTGCCTGTGAGGACTGATGTGTCCTGCCCAGCCGCAGCCCCCTAGGCCTGAAAGAACATCCCTTATGCCTCACTTTATTTCCTGTCCCTTTGTCTGTCTCTTGAGTGTGGGGCACCCTCTGTCTGTCCCAGTCTGTTATTACCCTGAATCTGGTTGTCTTTCCTCTCCACTATGAGCTCAGCACCCAATGCTCCTAGGCTGTCAGCAGGATGGGGCAAAGCAGGGATCTGCTGCTGAAGAGTGGGTCCGGCTGCGAAGGCTGGGGGGAGCACACTCTGCCAACCCTTTCCTTCTCCTGCTTTTCTCTCATAAATCAGCTGCTTACCCACTGCCTTCTCATCACTCACCCCTTCTCACCACCTCTCAACAG
Seq C2 exon
GGGATGGACGCAGAGCTCTTAGCTTCTTCCACCAAAAGGGCCTCCAGGACTTTGACACTCTACTCCTGAGTGATGACGGAGGCACTCTCTATGTGGGGGCTCGAGAGGCCATTCTGGCCTTGAATATCGAGGATCCTGGGGTGCCAAGGCTGAAGAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.250 A=NA C2=0.019
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(10.5=66.7)
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:
GGCTGAGCATGGCCCTTC
R:
ATATTCTTCAGCCTTGGCACCC
Band lengths:
310-2053
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]