HsaINT0147508 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48060778-48066420:+
Coord C1 exon
chr15:48060778-48060945
Coord A exon
chr15:48060946-48062693
Coord C2 exon
chr15:48062694-48066420
Length
1748 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
GTCCCATGTGTCTATTTCAGGTG
3' ss Score
12.41
Exon sequences
Seq C1 exon
ACATGGAGGTATCTTCATCTTCTGTTACCACAATGGCAAGTATCCCAGAAATCACACCTAAAGTGATTGATACCTGGAGACCTAAACTGACAAGCTCTCGGAAATTTGTAGTTCAAGATGATCCAAACACTTCTGATTTTACTGATCCTTTATCGGGTATCCCAAAGG
Seq A exon
GTAAGGCCTCAGCAGGGACCTCATCTCTAACTGCGTGGAAACCTGATCCTTAATGTCACTGAGGAGTATGTGGTTCTCCAGAGGTGGGCCTCACAGGAGCTTCTGCGGTTGTACCTCCACCGCCCCTTGCCACAGTCTCTCTGGCTTTCTGTGGTTATATCTGAGTGCATTCCTTAAAAGATAAAAGAGGTGGAAAGCTGTTGGAGAAAAGGCTGGTGAAGCAGCCACTCAGACAATCTAATCTGTGTTGATTTCTGTCTGAAGAAGCAGAGAGCCTGCTGGATTTCAGGGAATTTCGAGGGTCACCGCAGCAACATCAAAAAACAAAACTCATTAATTGCAAATATCCTGATATCAGATGTTTTGTCTAGGAGCCTTTCCCAGACTCTTGTTTAGCTTCAATTCAAAATGCAATCTGAAAAGGATATGTGAGATGCTAAGTTGCTTGAATGCCACAAGCAATAAAACATAACAGAGTGCTCGTCCATAACTATCATTTTCAGCCCGTAATAGGAGCAGTTATAAAATAGCTGCCTGTTGAGTTAGCTTATTAAATATATTACTCTAGGAAAAAAAAATCTATTCTTTAGTACTTACTAAACTATGGTATCAGGTTTCCAATCAGTTTTTATGGCAGCACATTGTCATTTATGATTTATATCGGTTGATTTTCATTTTATATGTTTTCGTTGTAACCAATTTTATAATCATTCTTCTTTCTGCTTTGCTTTCTTTAGTAACACCATTTTTTTCTACTTTTCTTTCTCGGTCTTTCACAGTGCCACTGAATTCCATAACATTAATTAAACATTAATTAAAAACAACTAATGTTCAAAGGCCTTAGTACTAACTTAAAGCAACAGAATCTTCAAAATCACTCTGACTTACCTTACTCTGGGATAGCTGTGTTTATAGCATGTAACAGACTTGAATACCTCTTAAACTAACTTTTTTTTATTAATTGTTAGATGTCTGTGGTTGCATTAAAAGGTTAAGTTTAATTTCAGTAATTATAAACTAATTTGCTCTTCTTTTTCTAGGTCTAATTTAAATATTTTCAAATATCTTCAGATAATTTGACAGTTTACTTAACTAATACATAGTATGTTTCCTTAGACTGTCTGGGTTTCTTACATAGTCGGTCATTCAAGAGTGCTTCACCCCAAGATGGAATGAAAAAAAAAATCCAAGCAAACATGAAAGTCTCTATTTATAGCTAACAGTGATCAAGCAGATATTTTTGGTTTGTGAACAAATTATATGTTCATATTAAAGTTAGTATAATTGTATCAGAGTAATTATTTTAGCATATGTTTATGCTAATTATTACATTTTCCTATATCCTAGTAGCTACCTTTTAATCCTGAATTAAGAGAAAATTATGAGACAAAACATATGAGTTTAAAGTTAGCTATTTAGAAAATATACACTTCTAACTATTTTTTAGATAGAAACTCTTACATTTTTAACATGTAACAACTATTTATGAGGGATTGGAGGAAAAGAACAGAAGAATACAGATCAGTGGGAGATTAGAGTTATCCTGGCATTTGCAGCAATCCTGTATGTCTCTGGGGATCCTAGTTTGATTAAAGACAAAATATACAAGGAATTTTGGAGTCTACTTGACCCTCCGAGCTAAGCATATGAACCATATGAAGGTCGTGTTGGCTCACTGAAAGCCATTTGCTATTTATTATTATTTTTAAAAAGCACCTTATTCACATTGTCCCATGTGTCTATTTCAG
Seq C2 exon
GTGTACGATGGGAAGTCCAGTCTGGAGAGTCCAACCAGATGGTCCACATGAATGTCCTCATCACCTGTGTCTTTGCTGCTTTTGTTTTGGGGGCATTCATTGCAGGTGTGGCAGTATACTGCTATCGAGACATGTTTGTTCGGAAAAACAGAAAGATCCATAAAGATGCAGAGTCCGCCCAGTCATGCACAGACTCCAGTGGAAGTTTTGCCAAACTGAATGGTCTCTTTGACAGCCCTGTCAAGGAATACCAACAGAATATTGATTCTCCTAAACTGTATAGTAACCTGCTAACCAGTCGGAAAGAGCTACCACCCAATGGAGATACTAAATCCATGGTAATGGACCATCGAGGGCAACCTCCAGAGTTGGCTGCTCTTCCTACTCCTGAGTCTACACCCGTGCTTCACCAGAAGACCCTGCAGGCCATGAAGAGCCACTCAGAAAAGGCCCATGGCCATGGAGCTTCAAGGAAAGAAACCCCTCAGTTTTTTCCGTCTAGTCCGCCACCTCATTCCCCATTAAGTCATGGGCATATCCCCAGTGCCATTGTTCTTCCAAATGCTACCCATGACTACAACACGTCTTTCTCAAACTCCAATGCTCACAAAGCTGAAAAGAAGCTTCAAAACATTGATCACCCTCTCACAAAGTCATCCAGTAAGAGAGATCACCGGCGTTCTGTTGATTCCAGAAATACCCTCAATGATCTCCTGAAGCATCTGAATGACCCAAATAGTAACCCCAAAGCCATCATGGGAGACATCCAGATGGCACACCAGAACTTAATGCTGGATCCCATGGGATCGATGTCTGAGGTCCCACCTAAAGTCCCTAACCGGGAGGCATCGCTATACTCCCCTCCTTCAACTCTCCCCAGAAATAGCCCAACCAAGCGAGTGGATGTCCCCACCACTCCTGGAGTCCCAATGACTTCTCTGGAAAGACAAAGAGGTTATCACAAAAATTCCTCCCAGAGGCACTCTATATCTGCTATGCCTAAAAACTTAAACTCACCAAATGGTGTTTTGTTATCCAGACAGCCTAGTATGAACCGTGGAGGATATATGCCCACCCCCACTGGGGCGAAGGTGGACTATATTCAGGGAACACCAGTGAGTGTTCATCTGCAGCCTTCCCTCTCCAGACAGAGCAGCTACACCAGTAATGGCACTCTTCCTAGGACGGGACTAAAGAGGACGCCGTCCTTAAAACCTGACGTGCCACCAAAGCCTTCCTTTGTTCCTCAAACCCCATCTGTCAGACCACTGAACAAATACACATACTAGGCCTCAAGTGTGCTATTCCCATGTGGCTTTATCCTGTCCGTGTTGTTGAGAGGATGATGTTGTAAGGGTACCTTAAAACAAGAGACTCGCTTGTATTTTAAGAGAACCAAGTGGCCAAAGAAACTCTTTCTAACTTTGGCAACATCAGAACTTGCCACATGTAGCTACTGCAGCAAGGCTTCTGTGTACTTGCCTGAAAACAAAGGAAGGTGCTGGTCATTCCATTTCTTTTGTTTGAAGCTAAAGAGATGTGTAGCTCACAGGGGCTACCTTACCAGTATAAAGAGCTGATAACAGTACTCAGAAGAATCTGTGAACAAATACTTGAAAATGGGTTCAATGTAGACTGCCATTATGTGTGGTCTTCCCATTAAATGTGAACATTTTAATATGTATGCATTCACCTTGCCTCTTGCACAAATGTCAAAAAAAAGATGGTAATATCTCAAAGAAATGAACTTGTAGATTACCAAGCAGTTTGCTAAAAATTCAATCTTTGACCCAAGCTGTAGCATTTTTTTTTCATGTGTGGCATCTTTTTCATGCCACCAACAAACTTGTTGTGTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCTGTACCCACTAGGATTTGTTTAGGTGCCCATTGCATCTTTTTGTGCTATGGAGTTGTTTACATTAAGCATGACCGAACGAGAGACAATACTATTTCCCACAGGAGTCCATTGGGTTCAGCTTTGAAAGAGGAATAGAATCGAGGCTCCTTTGACCATCAAAATGATGAACTTTACTTATGTGGTACCCAATGCCAGAATGTAAGAGTTGCAAGTGATTTTGTGCTGCTATTCATTAAAACTTGTATTCCAGTCTTGCCAGCTTAAGGAGATCAAGATATTAAGAGGTATCCTTGATTTATTTTCCAGTATTCAGTAGTAAAATTTTCCTGTCCACTGTGAATCAAAGCCTGAGTCACTCTATTTAACCTTGGACACACTAATAAGGTTTTATTTTGATTGTGTTCGTTTCCCCCCCCCCAATAGTAAAATTTCTCCTCCTTTAACTCCTCCTACCCCCCAAGGTAAGAAACAAAAAACAAACAAACAAACAAAAATAGAAGACAAAAGAAAGACATATGAAAGGAATTGTAATTGGCTTAACAGAAACAGTCTGTAAAAACCTAACAGTGGTGCAATCATGTTGTCTGTGTTGTGTTATGTGAGAATTTTCTCCTAAGTCATGCAGGTAATGACAATATACTGTAAATACCACATGTGAGTTTACCTGAATCTGTGCATTTTGTGCCTTATTCATGAGAATGATAGAAGTACTAAAATCTGTCAAGTGTTTTCAGTATAGCACATTATTTACTGAGTGCCAGTTGTAAATGTTTTTCAACCAGCACCTAAAAAGACTCTTTTCAAAAAATCACAGAAACAACCTAGGACAATTATTTGTTACATAATCCGACCTCATAGCAGCATTACATTCTTTGCCGTGATAAACATTCCACTCCTGCTTTCCTAAGGATGAAACAGTGATAATGTGAACTCAAATGAGGTTTCCTGGGTAATGTGACACCTGCAGAAACTATAGAGCGTCATTTATACGTAGTTTGGCAGAAACCACTTACGGCTGATGATGCGCAACCCTGCTGACTGTTTCAGTTAATATGCTGCACACCACACACTTGTTTAGTGAACCAAATCTAGAAAGTACCAAGGCAGAGGTATGCTCCTGCTGTAATCAGGCAAATGAGTTCAACTGGATTTCTTTTGACAATACTGTTGGTACCTATTACTTGGGGGAGGACATGTTGCAGAAGACCAGATCATTTTTATACAGAATGTGAAATACTGATACAGTTATTCTTTTTTTTAAAGAACATTGTTTTATAAAGAACGTGATTTCCAGTGATCTCTGGAAGCGCTAAAGCTAAAATTTCTGTTCTTGAAACACTTCAGCTTTGCAACTAAAATATTACAGATTAATAATAAATTAAACCAACCAATGATAAACACTACTCAGTCCACCAACAACAAACGTGTTTGAATTCACCTTACCAATATTAATCCCAGCGTGTGTAAAACAGAACAGTAACTCTATGTGACCCCAGATAACATTTTGTAACATTGTGCTTCCTTGTAGTTTGTAATGTGAGTTCAATCAGTATTTATGTTGAAATTTCTAACATTAAATCTAGTCTCTATCCTGTTAATTTAATTTTTAAATGCTTTATCCATTTGTGCAAAGGTAAACGCAGATTGTATCTTTTTTAATGGTACGGCATAAAAAGTAACCCTCAAGTGAAGTGTCTCTATACTGTTTTATAGAGTACTTTAACATGAATAGATACCTTGTAAACTTGTATTGTGGATGTGTAAATAATATGTACTTTGGGTTTTTAACACCGCATGTAAAGTCAAAATAAAATATACAAATCATTATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153618:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.790
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(13.6=75.0)
A:
NA
C2:
PF0143720=PSI=PD(13.6=2.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCACAATGGCAAGTATCCCA
R:
CCACTGGAGTCTGTGCATGAC
Band lengths:
344-2092
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)