HsaINT0147381 @ hg19
Intron Retention
Gene
ENSG00000187764 | SEMA4D
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:HGNC Symbol;Acc:10732]
Coordinates
chr9:91992152-91996013:-
Coord C1 exon
chr9:91995970-91996013
Coord A exon
chr9:91994545-91995969
Coord C2 exon
chr9:91992152-91994544
Length
1425 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CGTTTATTTTGATGTTCCAGATA
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGGTTTGATTCAGGAGATGAGCGGCGATGCTTCTGTGTGCCCGG
Seq A exon
GTGAGTGACTCCTCGACGTCCCATTTCCTTTGGGAGTGGCGAGGTCTTGTAGCCATTTCACGGTGCTTCAGTTCTGTGGCATTTGTGTGTGTTTTGTTTTTCTTTCTCCACTCGGAACAGAGGTCAAGTGTTCTGTAGCAGACTCGTGGTCTTCTCTGTCTTTTTTTCTTGCCGAAAGAGTACTTGAAGCCACTTAGAGTGTATCTGCTTACTGGGAAGCAGTCTCCTTCCAAAACCATCCTGTTTTCTTTCTGCTTAGCTTGGGGCTCATTAAGCAAAACCTAAGCCTGTTATAAATGGGGAGAAAGGAGCCCATGAGTGATTAATCCTCAGGCAGTGTAAGGGCTGGGGTGGTGTTTCCCCTGGGGCTCCCACCTGGGATTCACCCGCCTGTGGATGTCTGAAATAGCACCACACCCAGAGGGAGGGGTGGCATCAGGCCAGATGCCCCTTCCCCAGCAGCCACCTTCCAGGGTGCTAAAGGCAGACTTGACCCTCAGTTCTGTGTCTTCCTGACCCTGACAAGACAGCTGTCATCAGACTAAGAAAGGTTTAGGCAGCTGGGCATGGTGGTACACGCCTGTAGTCCCAGCTACTAGGGAGGCTGAGGCAGGAGGATTGCTTGTGCCCAGGGGTTCAAGGCTCAGTGAGCTTATCATGCCACTGCACTCCAGCCTGGGGTGACAAAGTGAGACCCAGACTCTAAAAAGAAAACAAAAGCTGGCCGGGCACAGTGGCTCATGCCTGTAATCCCAGCATTTTGGGAGTCTGAGGCAAGAGGATCACTTGAGCTCAGGAGTTCGAGACTACCCTGGGCAACGTGGTGAGACCCTGTCTCTACAAAAAATACAAAAATTAGCCAGGCCTGGAGGTGGTCACCTGTAGTCCCAGCTACTCTGGAGACTGAGGTGGGAAGATCCCTTGAGCTGGGGGGGTTGAAGCTGCAGTGAGCTGTGATTGCACCACTGCACTCCAGCCTGGGCAACAGAGCCAGACCCTGTTTCAAAAAAAAGAAAAAAAAGAAAAGTTTAGGCAGGAGGAGAGTGCTGAGATGCACTGAAAGGCCAGTCTTCCTTGCAGCCATTAGCAGAAGCGTCTCGTGTCTGATTCAAAGAGCTGACACTAGGCACAGAACTGGCCTCTGCTCAGCTTCCCCAGCCTGACGCGTTTTCTTCTGGGACACGGGTGAGAAATGGGATTTCTGCTGCTCAGAGCTGCCTCCAATTTCTTTGTCCCCATGGGCTGTCATCCAGGGCTCATCTTTGCTTTTTGGTCACGCATGTCTTTATCTCCTTAGTTGTTCTGGAAGATTCCATGTTGCTACAGTGGGTGAAACTCTTGCGTCATCTTGTGGGTATTTTAAAGAAGTTGTTAAATAGCAAATGGGGATTGTTGACGCTGTGCACGTTTATTTTGATGTTCCAG
Seq C2 exon
ATAAAAGTAAAGGAAGTTACCGGCAGCATTTTTTCAAGCACGGTGGCACAGCGGAACTGAAATGCTCCCAAAAATCCAACCTGGCCCGGGTCTTTTGGAAGTTCCAGAATGGCGTGTTGAAGGCCGAGAGCCCCAAGTACGGTCTTATGGGCAGAAAAAACTTGCTCATCTTCAACTTGTCAGAAGGAGACAGTGGGGTGTACCAGTGCCTGTCAGAGGAGAGGGTTAAGAACAAAACGGTCTTCCAAGTGGTCGCCAAGCACGTCCTGGAAGTGAAGGTGGTTCCAAAGCCCGTAGTGGCCCCCACCTTGTCAGTTGTTCAGACAGAAGGTAGTAGGATTGCCACCAAAGTGTTGGTGGCATCCACCCAAGGGTCTTCTCCCCCAACCCCAGCCGTGCAGGCCACCTCCTCCGGGGCCATCACCCTTCCTCCCAAGCCTGCGCCCACCGGCACATCCTGCGAACCAAAGATCGTCATCAACACGGTCCCCCAGCTCCACTCGGAGAAAACCATGTATCTTAAGTCCAGCGACAACCGCCTCCTCATGTCCCTCTTCCTCTTCTTCTTTGTTCTCTTCCTCTGCCTCTTTTTCTACAACTGCTATAAGGGATACCTGCCCAGACAGTGCTTGAAATTCCGCTCGGCCCTACTAATTGGGAAGAAGAAGCCCAAGTCAGATTTCTGTGACCGTGAGCAGAGCCTGAAGGAGACGTTAGTAGAGCCAGGGAGCTTCTCCCAGCAGAATGGGGAGCACCCCAAGCCAGCCCTGGACACCGGCTATGAGACCGAGCAAGACACCATCACCAGCAAAGTCCCCACGGATAGGGAGGACTCACAGAGGATCGACGACCTTTCTGCCAGGGACAAGCCCTTTGACGTCAAGTGTGAGCTGAAGTTCGCTGACTCAGACGCAGATGGAGACTGAGGCCGGCTGTGCATCCCCGCTGGTGCCTCGGCTGCGACGTGTCCAGGCGTGGAGAGTTTTGTGTTTCTCCTGTTCAGTATCCGAGTCTCGTGCAGTGCTGCGTAGGTTAGCCCGCATCGTGCAGACAACCTCAGTCCTCTTGTCTATTTTCTCTTGGGTTGAGCCTGTGACTTGGTTTCTCTTTGTCCTTTTGGAAAAATGACAAGCATTGCATCCCAGTCTTGTGTTCCGAAGTCAGTCGGAGTACTTGAAGAAGGCCCACGGGCGGCACGGAGTTCCTGAGCCCTTTCTGTAGTGGGGGAAAGGTGGCTGGACCTCTGTTGGCTGAGAAGAGCATCCCTTCAGCTTCCCCTCCCCGTAGCAGCCACTAAAAGATTATTTAATTCCAGATTGGAAATGACATTTTAGTTTATCAGATTGGTAACTTATCGCCTGTTGTCCAGATTGGCACGAACCTTTTCTTCCACTTAATTATTTTTTTAGGATTTTGCTTTGATTGTGTTTATGTCATGGGTCATTTTTTTTTAGTTACAGAAGCAGTTGTGTTAATATTTAGAAGAAGATGTATATCTTCCAGATTTTGTTATATATTTGGCATAAAATACGGCTTACGTTGCTTAAGATTCTCAGGGATAAACTTCCTTTTGCTAAATGCATTCTTTCTGCTTTTAGAAATGTAGACATAAACACTCCCCGGAGCCCACTCACCTTTTTTCTTTTTCTTTTTTTTTTTTTAACTTTATTCCTTGAGGGAAGCATTGTTTTTGGAGAGATTTTCTTTCTGTACTTCGTTTTACTTTTCTTTTTTTTTAACTTTTACTCTCTCGAAGAAGAGGACCTTCCCACATCCACGAGGTGGGTTTTGAGCAAGGGAAGGTAGCCTGGATGAGCTGAGTGGAGCCAGGCTGGCCCAGAGCTGAGATGGGAGTGCGGTACAATCTGGAGCCCACAGCTGTCGGTCAGAACCTCCTGTGAGACAGATGGAACCTTCACAAGGGCGCCTTTGGTTCTCTGAACATCTCCTTTCTCTTCTTGCTTCAATTGCTTACCCACTGCCTGCCCAGACTTTCTATCCAGCCTCACTGAGCTGCCCACTACTGGAAGGGAACTGGGCCTCGGTGGCCGGGGCCGCGAGCTGTGACCACAGCACCCTCAAGCATACGGCGCTGTTCCTGCCACTGTCCTGAAGATGTGAATGGGTGGTACGATTTCAACACTGGTTAATTTCACACTCCATCTCCCCGCTTTGTAAATACCCATCGGGAAGAGACTTTTTTTCCATGGTGAAGAGCAATAAACTCTGGATGTTTGTGCGCGTGTGTGGACAGTCTTATCTTCCAGCATGATAGGATTTGACCATTTTGGTGTAAACATTTGTGTTTTATAAGATTTACCTTGTTTTTATTTTTCTACTTTGAATTGTATACATTTGGAAAGTACCCAAATAAATGAGAAGCTTCTATCCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000187764-SEMA4D:NM_006378:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.097 A=NA C2=0.182
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(26.4=87.5)
A:
NA
C2:
PF0004720=ig=WD(100=18.8)
Main Inclusion Isoform:
NA
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:
ATTCAGGAGATGAGCGGCGAT
R:
GAACAACTGACAAGGTGGGGG
Band lengths:
358-1783
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)