GgaINT0067169 @ 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:43465495-43467162:-
Coord C1 exon
chrZ:43466940-43467162
Coord A exon
chrZ:43465611-43466939
Coord C2 exon
chrZ:43465495-43465610
Length
1329 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACATTGCTGTGTCATTGCAGATC
3' ss Score
9.36
Exon sequences
Seq C1 exon
TGTATAAACAATGAAGCCAGAGCCTTGAACTACGTGACTTCTCTGAATTTACCAGACAAAACGTTGCAGTTTGTTAAGGACCATCCACTAATGGATGATTCAGTGACTCCAGTGGGAGACAGACCCCGCCTTGTAAAGAGAGATGTGAAATATACGCAGATTGTAGTAGACAGAGTCAGAGCACTCAATGGTACAATATATGATGTTATGTTCATCAGTACAG
Seq A exon
GTAAGTTCTGCATAATATTATTTTTAATAATGTACTTATTCTTCAGACAGAAGTGTGCTCTAATGGAAACTCAAAATATTTACATATTTATGGTATTTTTACAGTATGTGGTATTTTCATAGAAAAATGGGGGGCCACAATAAGTACATGGAGAACCTTGCTTGCTTTGAGAACCTGTTGCAGGAGGAGAACTGAAAAAACCCAACTTTATCAATGACATTGACAGTGGGATTCAGTGTACCCCTCAGCAAGTTTGCTGATGACACTAAGCTGAGTGATGCAGTTGACAAAGTGGAACTGGAGGGTTGCCATCCACAGGGACCTGAATGGGCTTGGAAAGTGGGCAGATGAGAATCTAATGAGGTTTAACAAAGCCAAATGCAAGATACTGCACTTGGGTCGAGGCAATCCCAGATGTGTGTGCAGACTGAGAGAACTTATTGAAAGCATCCCTGTGGAGAAGGACTTGGCAGTCTGATGCAGTGTGTTCTTGCAGCCTGGAAGGCTAGTGGTATCCTGGGAGGGGTGACCAGCAGGTTGAGGGTTCAAGGTGATTGTCTCCCTCTACTGTGCCTTTCTGAGGTCCCATCTATAGTACAGTGCCCAAGTATGGGTACAGGGAGAATGTGAAGCTATATCAACATCTCCAGAGAAGGGCCACGAGGATGTTTAAAGGGCTGGAGCACCTCTCCTATGAAGAAAAGTTGAGTAAGTTGAGCTTGGAGAAGAGAAGGCTCCAGAAAGAGCTCATTGTGGCCTTCCAGTACTAAAAAGGAGCTTACAAGCAGGAGGGGGAGCAACTTTTCACATAGTCTAAAAGTGATAGGGTGAGGGGGAGAGGCTTTGAACTCAAGAGGGGAGATTTCAGATTAGGTGGTACTCAGAAATTTTTCACTCAGAGGGCAGTGAGGCACTGGCACAGGCAGCCCAGAGCTGTTGTTGACACCTCATCTCTGGAAGCATTCAAAGTCAGAAGTGATGGCACCCTGGGCAGGAGCAGTCTGGTCTAGTGAGTTCCAGGCCTGTCCATGGCAGGAGGTTGGAACTGGCTGATCCTTAAGATACCCTCCATCCTAAGCTATTCTGCAAACTGCAGAACTGTAGTGTTTTGCGTAAACATACATGAGGTAATCCCTGAAAGCCATTCTTCATTTCAGAAGGCCTTCTCTTTTCCAGAACTCCTTACAGTGACAGGTACAATGTTTACCATTGACACAGGCTGGCGTGAAGTCTCAGCTGGATAAGTGATGTAAATTGTAGCAAGTGTGCTTTTTTACCTGCCTTTTTATTTTAAGAATCTCACTTAAATACATTGCTGTGTCATTGCAG
Seq C2 exon
ATCAAGGGGCCCTGCACAAAGCTATCAGCTACGAAAATGGAATGCATATTATAGAAGAAACACAACTTTTCCCAAAGTTTGAGCCAGTTCAGACACTCTTACTTTCATCCAAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000037939:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(8.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTATAAACAATGAAGCCAGAGCCT
R:
TGGATGAAAGTAAGAGTGTCTGAACT
Band lengths:
334-1663
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]