HsaINT0147521 @ hg38
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
semaphorin 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr15:47762200-47763104:+
Coord C1 exon
chr15:47762200-47762319
Coord A exon
chr15:47762320-47763015
Coord C2 exon
chr15:47763016-47763104
Length
696 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCT
5' ss Score
8.49
3' ss Seq
GTTTTTAATTTTTCTTTCAGAGC
3' ss Score
10.22
Exon sequences
Seq C1 exon
ATGGGAAGCTGTATTCTGCCACAGTGGCTGACTTCTTGGCCAGCGATGCCGTTATTTATCGAAGCATGGGTGATGGATCTGCCCTTCGCACAATAAAATATGATTCCAAATGGATAAAAG
Seq A exon
GTACCTTTGAAGAGCAGTGTCGTGGGGTCACCAGGATAGTGGATGGCCCAAGTGGGGACAGCAGCCACGGCCATCAAGAGGTTCAGCGCATGACTTTATATTGTTTATTTAGAACAAGTACACACTGCTTTGATTGTGAACAGGAGCATTGACAGGGAATGAGGAGGCTGGTAGCCATGTCAGAAGAGTAAGTTCATCCAGGTGTTTATCCTAGGTGACCTCAAAAAAAAAAGGGGAGATTTCATCTCTGTGTGTGCCAATTTGTCTAACTTTCTAAATGCACATAATACTACTTGCCATCTACCCATCTTGGAAAGTTACCAGAGAGAATCGATTAGTCCGTATGAGAGCCATTTTGTTCTTCAGAGTCTAGAAATCAAGATTTTTTATTTTCAGTGTAAGAGGTTTTCTTCCCTAGTTAAATAGGTTAATGAATAAATCTGTTGAAACAAAGACCTTTGCTGTAGTTCAGTTCCCTGTAGGTCTTTTTACAGTCCATTAGCTGACTTTAGAGATGACTGGTTCCCTGAAGCTTGAACACACCCATATTGGGACTCCTCAAAGTCATTGGCAGATTGGAGTTCTTGTTGGCTTGAATGTAATTGTGCAACATCTGTCAGTCATGCTTTGCAGTCGGGGTCTTATGCTAATTGAATTATCCTTTAGGAACCAGTTTGTTTTTAATTTTTCTTTCAG
Seq C2 exon
AGCCACACTTTCTTCATGCCATAGAATATGGAAACTATGTCTATTTCTTCTTTCGAGAAATCGCTGTCGAACATAATAATTTAGGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872:ENST00000558014:11
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=PD(24.1=95.1)
A:
NA
C2:
PF0140314=Sema=FE(6.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGGAAGCTGTATTCTGCCAC
R:
TGCCTAAATTATTATGTTCGACAGCG
Band lengths:
206-902
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development