HsaINT0147507 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48059234-48060945:+
Coord C1 exon
chr15:48059234-48059290
Coord A exon
chr15:48059291-48060777
Coord C2 exon
chr15:48060778-48060945
Length
1487 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
AAATCTGTTTGCCACCACAGACA
3' ss Score
5.36
Exon sequences
Seq C1 exon
AAATTTTGCCTACTTCAACTACACCAGATTACAAAATATTTGGCGGTCCAACATCTG
Seq A exon
GTTAGTTTTTTTTAATTTTTTTGAATTAACAACCTTTTCTTTCCTTCAGTTCAGCATTTTCAGCCCCTTCTCCCCTCCTTTTGCGCAGTTTGGCAGCCCTTCATTTTTCCGCTTTGACTCATATTCCCACTGATGGTACCAAAAGACTTTTCTTACTGAGCACTTCACCCTTGTTTATAGCATGTTAACACTTCATCATTGACCAAGCCACATCCTTTAAGAAAATTCAAATGGGCTAACATAGACTGCATTCCAGCTGCACGCACGCCCACCCAAGCTTTCTTCTTTCTCACCTCTTTGCATTGTGAATGTTTCTTCTGGTCATCTGTATTTAATGGATGGCGGAATTTCATTATTTTCCCCATCTCTCCTCACCTTTCCTATGACCTAGTAAACAAATACACATTTCCCATAAATGTGTATTTATAAGTTTTAGAGATCTTTGAATGGTTTGCGCTAATCCTGGGAATCTTTGAATGTTGTGGTCTCAGTGGTGTGAAAAAGGCTTCAGTGGAGTGAAGCTGATTTTTGATGTATTAAGATGTTCAATGGGCTCTCCAAGCCTCTCTGTACCTGTTTGGAGCCTCCTTCTGTTAACTGTTGCACCAGTCAGAATTGTGGTCTCTGAGGTTTTAGCTTAAAAGCGTAGGCTTACATTTTGAGGGAAAATCTATTTGGAGGAAATCAGTACTAGACATGCTAAAAGGTTAAGTTAACTCCCGGTCCTATTGCTGCTTCTAAAACTCACCAGCAATTCCTTTCCTCAGGGGGAGAAAAAGATGGTAGATCTTATGTATCAGAATATCCTCATTCAGTTTGTAAATGCCATTGCCTTTGCATTAGGTTCTGCTTGGAAGAAACTCCCCAGCAGTTTTGGAGAGAGTACAAGCAAAGTCTGTCCCCTCCTTCGTTGTTTTACTGTGGGTGGCAGAGCCTTAGTATAGTGAATAATCTACAAATGGACAGGAGCCCCTGGTAACAACCTCTTAGGCAGAGCTGGTTTGTCACGTCCAAAATCAAGTATTTTCATAGACTTAACCAGATATTTTCCAACAAAGTTCCATCATAGCTTCTTCCCCAGTAAAGCCTATAGATTTTCTAACCATCTGTGAAAGTGCTTTTAAAAATGCATAAAAAAGAAATGAAATGATGTCTCACAAGAGAAGGAAGAAACAGCAACTAATCTGCCCTGGGAATTATATTACCTTTTTCATGAGTGTCATTAGTAACCACAGGGGCTTTCCTAAGAGCCTTTCGAGTATCTTTAATTTTGAAATCTGCTGAATATGTCTTTACTGTTAATTTTTAGTTTTCATTCTTCCCTTGAAAGGAAGGAATTTGATGTAGCTTCCTCAGGCGTGTTTTTACAAAATCCTAGAGCAAACTTTCTCATAAAATTTACTCAAACTTTATTTAAAAATGCAACAGACCAATCAAAAAAAATCTTGACACTATCCATATTAATAAAAATCTGTTTGCCACCACAG
Seq C2 exon
ACATGGAGGTATCTTCATCTTCTGTTACCACAATGGCAAGTATCCCAGAAATCACACCTAAAGTGATTGATACCTGGAGACCTAAACTGACAAGCTCTCGGAAATTTGTAGTTCAAGATGATCCAAACACTTCTGATTTTACTGATCCTTTATCGGGTATCCCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153618:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.076
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(5.0=15.0)
A:
NA
C2:
PF0143720=PSI=PD(13.6=75.0)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCCTACTTCAACTACACCAGA
R:
GGATACCCGATAAAGGATCAGTAA
Band lengths:
214-1701
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)