GgaINT0066657 @ galGal4
Intron Retention
Gene
ENSGALG00000010697 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:HGNC:10732]
Coordinates
chrZ:43446918-43448867:-
Coord C1 exon
chrZ:43448664-43448867
Coord A exon
chrZ:43447016-43448663
Coord C2 exon
chrZ:43446918-43447015
Length
1648 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
ATCCCATTTACAATTTTCAGATA
3' ss Score
7.24
Exon sequences
Seq C1 exon
GTCCAGATGACTCCCATTTTGTCTGGAAGAAGAATGGACAGGAAATGAAGGCATGCATCACTGAGCAGGCTCACAGGCTGTTTGATGGCAGAGTGCATGTCTTAAGTTGGGTGAAAGATTCAGTATCAGGAAACACAAAATATAAATGTTCATTCATCTCAAGGATTGGGAACACAACATCAGAAGTGCTCATCAAAGTGGAAG
Seq A exon
GTAGGCTGGTTCTGACTGTATGCTTTTTGTATTATCCATGTATATGTGTTGCTGCTAACTCTCCTTTGCTCTACTAAAACCCACCTCCTTTGTTTATGAAAAGGTTTTGCAGACACAGAAAATTGCTTCTTCCTCACCCTCTTATAGAACTAACCTGTATATCAGCAGATATACACTAGAAATGAAACTAAAACTGTTAAACTAATTGACACCAATTTTATGCGAGTACTGAAAAAAGAATATAAAATAGCACTCTGCAGGAACTATGCAGGGTGACAAAAACCTTTACTTCTAAGGAAGTGATAAAAAGAAATGCCCAGTGCATGGGAATCGTTACATCACGGCCTGAACCAGTGACTGAGCACCTGATGAAAAGGCATGGCAAGCCCTGGAAGCACAGGTGCAAACAATTCACCTGTGCAACCCTGGGCCCACCCTCCTCCCTAACCTCATTTAAGGGCTAGCAGCTGAGGGAGTAGCATCTCTGCTTACAGATTGTCTCCTCTGGTAGTTTTCCAGTCAGCCTGCATGTTTAGAATGGGGTAAGCTATTCCTTCCTTATTACTGGATTGTGACTAATACCTTTCTTGCGCTACCGAAAAGCTGCTCAGAGGCAATCATTTATTTCATACCATGCACTCACAATATGGGATATTTAAAAATTGGGTGATCTGTGAATTGCCTGTAGTCAGGTGGATGCAGTTCCAATTTCTTCATTTTGCCACTCATGGGCCAGAGGTCAGACAGCTCAGCTGAGCACCTAGGTAAGATGTTCGTGCAACTAGAACTGACAACCTGAGTACCATTTGCAACTAAGTTTTGAGAACTTAATACCTGCAGAAAGTCTGAATAGATCTTAAATAATAATAATAATAATAAAATCCCAGGAGCAACAAAGGTAATGTGTTTTTGTTGTTGTTGTTTTCGTTTGTTTTTCTAATATGGAAAAGAAAAAAAAAATGTATTTACCTGATCAGTACTAAATGTGAATCTGTCAAGAACAGCTCAGCGTAGCCCTCTTCAGTAGCAAAGGAAAGCAGAATGAAGAGTATCTCAGTGAAACTGCTATCAGTGTAAAACGGGTGGCTTTAAAAGCATTATACCATGATTATCCTGACAGATTAAATATTACATCTGTGTATGCTGCTACCACCACAGTGGAAGGGACTACAAGGAAAACTTCCTCAAGATGTGGTAAAGCAGTCCATCCTATGCTCTGAAGTATGGAATAAAGAACAACTCACTACATAACATTACTGTAAAATGGGGAAATCACAAACTGGACAGTCAGCTGTATCATGTTCTTCTCTTCATCCTTGGCATGATGCAACTGCAACATTCCTGTGCTTCTAAATGGCTTAAGCCTGTGAGTAGGATATTTTTTTTTCCTAGAGTTGAACTGAAAGATAAAAGCACTGAGTCTGTTCACACCAGAGGTTGTAAAGTTTGCTGCAGAGGGGGAGAGACCAGACCATTTGAACAGAACTTATTTCCATGTAACCTAAGAGAAGGCAGAGCTGAACAGAAGATAAAATGGTGCCTTGCCTTCCTTTGAGCCCAATCCTCCATAAAAAGCACTGTGGCTGAGTTGATGTCAGCTTATTTGATCACTACTTGGTTACATAATCATCCCATTTACAATTTTCAG
Seq C2 exon
ATAGTGTTGGTAAGGATGGATGGACCAAAGAATTTGATACCTGGAGAACTGCTATCAGTGAACATGACAAGATGATGCAAAACTGGAGGAAGACATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000037939:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PD(72.5=95.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGATGACTCCCATTTTGTCT
R:
CCATGTCTTCCTCCAGTTTTGC
Band lengths:
302-1950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]