BtaINT0130797 @ 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
chr3:14675793-14677314:-
Coord C1 exon
chr3:14677154-14677314
Coord A exon
chr3:14675856-14677153
Coord C2 exon
chr3:14675793-14675855
Length
1298 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
TTCCCAATGCCCTACTTCAGATA
3' ss Score
6.31
Exon sequences
Seq C1 exon
GGGATGGACGCAGAGCTCTTAGCTTCTTCCACCAAAAGGGCCTCCAGGACTTTGACACTCTACTCCTGAGTGATGACGGAGGCACTCTCTATGTGGGGGCTCGAGAGGCCATTCTGGCCTTGAATATCGAGGATCCTGGGGTGCCAAGGCTGAAGAATATG
Seq A exon
GTGAGAGGCCAGGGAAAGGGTGCGGGCTGGAAGTGAGGAGGGGGCTGGCAGCTGCCCTGTGCCTGGACTGCCTATGCATGAATAACTACCCAATTTGCTGTTGCCTATAATCAGCAACGATTGGCAGGTCTTGGTGTGGACATATACACGTATGATTTTTATGACAGACAAGAAACACAAAAAAAATAAAAAAATAAAAAAAAAGAAAGAAAGAAACACAGCAGTGGCCTTACACTTCATGGGCACGATGAATACTGGTTGAATAATACTAATTGATAAAATGGCTGATACGGAAATTGACAAAGTGAAAGTGAAAGTTGCTCAGTCGTGTCCGACTCTTTGCAACCCCGTGGATAGTCCCTGGAATTCTCCAGGCAAGAATACTGGAGTGGGTAGCCATTCCCTTCTCCAGGGGATCTTCCCAACCCAGGGATTGAACCCAAGTCTCTTGCATTGCAGGCAGATTCTTTACCAGCTGAGCCACCAGGGAAGCCCAAGAATACTGGAGTGGGTAGCCTATCCCTTTTCAAGGGCCTCCTTCCCAACCTAGGAATTGAACCAGGATCTCCTGCATTAGCAGGCGGATTCTTTACCAGCTGAGCTACCAGGAAAGCCCCAATACTAGTTGCTAAAATGACTGATATGGAAATTGACCTATGAGAGAAACATTGACTCAAATTTATCAATAATGTGATATCCACCCACTGGAAGAAATCACTGAGGCTTCTGTGTTATAGTCACCCTACTCACAGGAATAATGTAAGGGAGAAAGGGAGAGGGAAGGAAAAAAGGGAGGGAGGGAGCAATTACTGAGCATCTCAACACAGTCTGTGTTGCTCAGCATGTGGTCTGTGGGCCACCTGCACATATGGGATGCGGATTAAAAATACAGTTTCTCTGAGGTGTGAGGAACCGAAAATTTTTAACAATTTCCCCAGGAAATGTGTTTTGTTTTGTTTCCAGCTGCTGCTTTGTATACCATGCATGGCATTAGGTGCTTTACATACAGAAATCTGTGCCATTGACCAAGATCACTCAACCAGTAAGTGGTTGAGTCTAGGTTCAAGCTCAGGTCTGATTCCATTGACCATGTTCTCACATGGAGCTGTGTCCTCATGAATATGAGTATCATTAGAGTAATAGCCAGGGTCACAAAGCGAGGTTCTTACAGCCTACCAGCATGTAACTAACCATTATGCCTGCTGGTGATTTCACACCAGAGCCAAGGAGCGGGTAGTAGGTCAGAGAGCTCAAGATCTCATTCCCTTCATCTCCCCTTTCCCAATGCCCTACTTCAG
Seq C2 exon
ATACCCTGGCCAGCCAGTGACAGAAAAAAGAGTGAATGTGCCTTTAAGAGGAAGAGCAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012228:ENSBTAT00000016223:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(10.5=66.7)
A:
NA
C2:
PF0140314=Sema=FE(4.8=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:
GATGGACGCAGAGCTCTTAGC
R:
CTCATTGCTCTTCCTCTTAAAGGCA
Band lengths:
222-1520
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]