GgaINT0067165 @ galGal3
Intron Retention
Gene
ENSGALG00000010697 | SEMA4D
Description
NA
Coordinates
chrZ:42889830-42892087:-
Coord C1 exon
chrZ:42891974-42892087
Coord A exon
chrZ:42889982-42891973
Coord C2 exon
chrZ:42889830-42889981
Length
1992 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TCTTCTTTTTGTATTTGTAGAAC
3' ss Score
9.18
Exon sequences
Seq C1 exon
ATGAGGAGCTTTATTCTGGGACTTCTTACAATTTCTTGGGAAGTGAACCTATTATTTCACGAAATTCTCATCAGAGTCCTCTGAGAACAGAATATGCAATACCTTGGCTTAATG
Seq A exon
GTAAGTGGGTGTGAGAGCACACCAGATCAAATTATTATTTCCTTTTTCAGTGTTACAAATTCAGACAAAGAGTTTGAGCTTCCTTTTGAGGCAAGAATCCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGAGTTTGAGCTTCCTTTTTGAGGCAAGGAGCGGTTGTTCACTGTCTCAAAGAGGGTGACTTCTGTTATATTGGTGTGCCAATCTGGTGTGCAGATTTTTTTTCTCTTTAAAATTTCAGAACTTTTATCAGTACTAACAATGAAAACAGCTTATAGACACACAGACTTTGACTGTCAAGTACTGTGTTTTACTTTATATCCATTTGTTCATCCTTGCTATGATACAACATACTTATAATGCAGTAAGAAGAATATTCCTTGTCCTCAATATATATATTTTAAAACCAATATGTTCTTGGTTCCTGATTATCTCAGTTCTTGACTTTCAGAACTGGCCAAGTTTTGTGAACTCTCAGAATTTTGTGGCTCTTGGCCCAAAAAAGACTAAAATCATGAAGTCAGCATATTGCCAAAAAAAAAAAATATATATATATAGCATCCAGAAAGGAGAGGATGCTGAGTACATCCTGTTATTATTGCTGTATTTGGTATTTCAGTTAGCAGCAGAAGTACTAAGTGGCTGGTATTGTGTACATGTAGTTAAAATCAAATGTTTTTACAAGATGGAGTTGACCTAAACCTTATATCTGATTTTATGCATGAGGGCTGGATGACAACAATGAGAGTATGCATGTTTGAAAACCAGGAGAAGACTGTGTGGTCTTCATATGTGTCCAGCCAGCTGCTAGATTTGCAGGTGCTGGTAGCTGACCAACCCTGGCAAATCATTGCTTGTAAGTTTTAGCTAATTCTATCCTTAAATACAAATGAACAGAAATATACCATATGCCTTGTCTTAAGTTTGCATCAGGGAAGAGAGGTAGGCAATGGAGGATAGGTATCCAAATCAGTGTTTCAATGTGGTTGAAAAATGAGGAGTAATGAGATACAACAGACTAAGAGAGAGATCTTTAAGGTATGGTATGTTAAATAGCTGGTTTTTTTCCTCCACAATTGTACTTTTTTAGAAGTGTTAATCATGGGCTCAACAACAAATAGTGTAGGCAGATCAGTAGCTGAAGATCAGTTAAATGTGGTGTAAGGTTTGGGAGAAGAAAATTCCTAGAGAGTCTTCAAGAGAATGAAGTTAAAAGAGTTGTTTATAACGTAAAATTCTTCTTTTTGTATTTGTAG
Seq C2 exon
AACCAAACTTTGTTTTTGCTGATGTGGTAAGAGCAGATCAAAACAGCACAGATGGAGAAGACGACAAGATATACTTCTTTTTCACCGAGGTGTCTGTGGAATATGAGTTTGTTGGAAAACTTATGATTCCGAGAATAGCTAGAGTATGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010697:ENSGALT00000017396:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(23.3=100)
A:
NA
C2:
PF0140314=Sema=PU(11.8=96.8)
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:
TGAGGAGCTTTATTCTGGGACT
R:
TGCATACTCTAGCTATTCTCGGA
Band lengths:
263-2255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]