MmuINT0141296 @ mm9
Intron Retention
Gene
ENSMUSG00000027200 | Sema6d
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:MGI Symbol;Acc:MGI:2387661]
Coordinates
chr2:124486441-124488107:+
Coord C1 exon
chr2:124486441-124486497
Coord A exon
chr2:124486498-124487939
Coord C2 exon
chr2:124487940-124488107
Length
1442 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
TCATCTGTTTGCCACCACAGACA
3' ss Score
7.08
Exon sequences
Seq C1 exon
AAAGTTTGCCTCCTTCAACTACACCAGATTACAAAATATTTGGCGGTCCAACATCTG
Seq A exon
GTTAGTTTTTTTTAATTTTTTTGAATTAACAGTCTTTTCTTTCCTTCAGTTTAGCATTTTCTGCCCTCTTCCCCACCCCCCTCCTTTTGCGCAGTTTGGCAGCCCTCCATTTTTCTGCTTTGACTCATAACCCTCTGAAGGTCCTGAGAGATGTTTTCTTACTCAGCCCTCCACCCGTGTGTAGCATGGAATGGTTCATCATTGACCAAGGCACATCCTTAAGGAAAGTCCAATGGGGTGACATATTCTGCATTTCAATTGCACGCCAGCCACCCAGCTCCCTTCTCTCGACCCTTTGCATTGTGAATGCTCCCTCTGGCCATCTCTATCCCATGGATGACAGAATTGCATAATTTTCCCCTTCTCTCCCCACCTTTCATACAAACAAGGAATGAACAATACACATTTTTCAAAAATGTGTATTTTTAAGTTCTAAAGATCTTTTTTTGAATGTTTTTGTGGCAATCCCAGGAATCTCTGAATGTTGTGTTCTCAGTGGTGTGAAAGAAGCTAGCTTCAGTTGAATGAAGCTGGATTTTGATTTTCTAAGATGTACCGTGCACATCTATCTGTGTTTGTTTCGAGGTCTCTTCCTGTAACTATTAGGTCAGTCCGTACCATGTCTAAAAGCGTATGCTTATATATTCATGGACATCTACTAGGCTAAAGCTCGCAATAGACACGGAAAGGTTCAGTTGCTCCTCAGACTATGCTGCATTAGGGGTCACATCAGTTCCATCTCTCAGGGGGGAGAAAAGGATGGCCTGTCTCATGTATCCCAACATCCTTATTCAGTGTATACATACCATTGCTTGTGCATGGGTTACTGCTAACTCTTTGGAAGAAACTCCCCAAGTATTTCGGAGAACACAGCAAGGTTTGTGGATGGAGTCTCACGGTGCATTGAGAAACCTACAGATGGACAGAGAGGCCTTGGGGAAGCAGAATGGCGGCCTCTTAGGCAGAACAGGTTTATCAGGTCCAAGACCAACTGTTTACTTGGACCTGACCAGATATTTTCTAAATGTAATTCCATTATAGCTTCTCCGGGGAAGGAAAGCGTATAGAGACCCCAGCCGTTCACAAAGGTCCTCTGTACATTACACATCACAAATAAATGATCCCGAGAGCTAGCTGGAGAGAGCCAGAGTCTGCCCAAGTTGGGGCTTAGGATACTTTTCCACGAGGAGGCTTCATTAGGAATGTTCACCTGTCTTTTACTTTGGAAATCTGCATAATGTGTCTTCATTGTCAGCTTTTAGATTTTACACCTCTCTTGCAAGAAGAAAAAAAAAATCTGGTTTCGTTCCCCTGAGGGGGCTTTTACCAAATTCTAGGACAGGATTTCTGAGAATACGTACTTGACTTTCAAATGCAAGGATGCAATCAGAAAAGTCTTCTTGACGCTAGCCATGTTAATGGTCATCTGTTTGCCACCACAG
Seq C2 exon
ACATGGAGGTATCCTCATCTTCTGTTACCACTGTGGCAAGTAGCCCAGAAATTACATCTAAAGTGATTGATACCTGGAGACCTAAACTGACGAGCTCCCGGAAATTTGTAGTTCAAGATGACCCAAATACTTCTGATTTTACTGATACTATATCAGGTATCCCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027200-Sema6d:NM_199241:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.150 A=NA C2=0.049
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(12.3=40.0)
A:
NA
C2:
PF0143720=PSI=PD(14.9=17.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTGCCTCCTTCAACTACACCA
R:
CAGTAAAATCAGAAGTATTTGGGTCA
Band lengths:
198-1640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: