GgaINT0067168 @ galGal3
Intron Retention
Gene
ENSGALG00000010697 | SEMA4D
Description
NA
Coordinates
chrZ:42884451-42885592:-
Coord C1 exon
chrZ:42885436-42885592
Coord A exon
chrZ:42884674-42885435
Coord C2 exon
chrZ:42884451-42884673
Length
762 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
CTTCTATTTTTAAATAATAGTGT
3' ss Score
4.77
Exon sequences
Seq C1 exon
GAATAATGTGGGTCTGTCAGCTGTGTGTGCCTACAATTTGTCTGCTGTAGAAGAAGTTTTCTCAAAAGGAAAGTATATGCAGAGTGCCACAGTAGAACAGTCCCATACTAAGTGGGTACGGTACAATGGGGAGATTCCTAACCCTCGACCTGGTGCA
Seq A exon
GTAAGTGTCTGTAATTTTGGATATGATATACAAGAGTAAAGAAACTAGAAAAGCAAACAAACAAACAAACAGAAAAAAAATACAGTGAAAACAAAAAAGCCCTACTAGAGTGTGATATTAGATTGCAGTGATCTGGATACTTTGTAAACATTTCCTGAAAGACACTTTAAGTGATTTATTCCAAAGTTTGTATTTGGGAAGCAGTGCTTTTTTTTTAAACTTACCATACAGTTAATTGCAGTTTTTATATTTTCATTATTTCATTACTAAATTTCTAGTGATGAAAAAGATAATAGTATACCTTAGGGAGCATTAGAGATTTTTTTAGTTCAAGTGAACAAAAGTGTAAAAATTGTTGCATTGTCTTACTAGGTCCAGCAAATTTAATCAGTGCAGTGTATTGCTCTGCAAGCTAAAATGCTCATAGTCCTGGGTCTCTTTCACACTCATAATTCTTGCAGTTGTCTTATTGCAATGGATGAGTAGGATTACAATTAAAGGTAATTAAGAAGCATAGGAATCCATAAAGAGTATTTTCCTATATTATATTTTGGGTCCAAATAAAAATGTAATATGAACCATTTGCTTAGAGATCAGCATATTGCAGAAGCCAAGGTGCTGTGGAACTTGAGTACCTTCCAGGCTTGGATGAATACAATGTACAGTTATGTCCTTATGTGCAGAAGAAAATGCATGTACCTGCCACTAGGATATAATTTGCTTTTCTCTCTATTATTTCTTTCTTCTATTTTTAAATAATAG
Seq C2 exon
TGTATAAACAATGAAGCCAGAGCCTTGAACTACGTGACTTCTCTGAATTTACCAGACAAAACGTTGCAGTTTGTTAAGGACCATCCACTAATGGATGATTCAGTGACTCCAGTGGGAGACAGACCCCGCCTTGTAAAGAGAGATGTGAAATATACGCAGATTGTAGTAGACAGAGTCAGAGCACTCAATGGTACAATATATGATGTTATGTTCATCAGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000017396:9
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=0.040
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.0=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGTGGGTCTGTCAGCTGTG
R:
CCATTGAGTGCTCTGACTCTGT
Band lengths:
344-1106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]