MmuINT0141102 @ mm10
Intron Retention
Gene
ENSMUSG00000028064 | Sema4a
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A [Source:MGI Symbol;Acc:MGI:107560]
Coordinates
chr3:88435959-88437900:-
Coord C1 exon
chr3:88437803-88437900
Coord A exon
chr3:88437253-88437802
Coord C2 exon
chr3:88435959-88437252
Length
550 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
ACCTCTTTTCTCTTCTCCAGTTA
3' ss Score
11.17
Exon sequences
Seq C1 exon
GCCTTGGAAGCAGGACATGGAACGCGGCAACCCGGAGTGGGTATGCACCCGTGGCCCCATGGCCAGGAGCCCCCGGCGTCAGAGCCCCCCTCAACTAA
Seq A exon
GTGAGTGTGGGACTGGAGGAGGTAACCAGGCACTTGGGGAACTTCGGGCAGGACTGGCTTTTCTGCTCCATAGCTTCTGTAGCACCTGCCTAGGCTGCAACCTAGCTTCCCGAGTCGCGATGTGAAGTGGACTGTGGACGGGAAAGGCATGCTGAGCTGGAGGGCACACTAGGGTTCAGGTTGAGGTCGATGTAGCCTTGGTGTCTGAGTTGGAGTTATTAATACTGGAGGCTGCCTACAGCCATGCCGCTCTGAACAGGATGGATCTTGACTGATCTCAGAAGCTAAGGGTTAACCTGGCTAGAAATTATACAGAGAAAGAAAGACTGAGGGCTAGTTTGGAGTTTAGGCTGGAGACAGAAGAGGGTTGAGCCTTGAGCTTGGGAGTTGAAATGGAATCCGAAGACAGATGGGCATGGTGGTCCATAGCAGGAATCCCAGACACCAGGATTACTGACCTGGGCTACAGAGTGAGACAGATGTAAGGCTGGCTCTCCCACCTTCCTTCCTCCCTCCCCACTGAACATGTCACCTCTTTTCTCTTCTCCAG
Seq C2 exon
TTAAAGAAGTCCTGACAGTCCCCAACTCCATCCTGGAGCTGCCCTGCCCCCACCTGTCAGCACTGGCCTCTTACCACTGGAGTCATGGCCGAGCCAAAATCTCAGAAGCCTCTGCTACCGTCTACAATGGCTCCCTCTTGCTGCTGCCGCAGGATGGTGTCGGGGGCCTCTACCAGTGTGTGGCGACTGAGAACGGCTACTCATACCCTGTGGTCTCCTATTGGGTAGACAGCCAGGACCAGCCCCTGGCGCTGGACCCTGAGCTGGCGGGCGTTCCCCGTGAGCGTGTGCAGGTCCCGCTGACCAGGGTCGGAGGCGGAGCTTCCATGGCTGCCCAGCGGTCCTACTGGCCCCATTTTCTCATCGTTACCGTCCTCCTGGCCATCGTGCTCCTGGGAGTGCTCACTCTCCTCCTCGCTTCCCCACTGGGGGCGCTGCGGGCTCGGGGTAAGGTTCAGGGCTGTGGGATGCTGCCCCCCAGGGAAAAGGCTCCACTGAGCAGGGACCAGCACCTCCAGCCCTCCAAGGACCACAGGACCTCTGCCAGTGACGTAGATGCCGACAACAACCATCTGGGCGCCGAAGTGGCTTAAACAGGGACACAGATCCGCAGCTGAGCAGAGCAAGCCACTGGCCTTGTTGGCTATGCCAGGCACAGTGCCACTCTGACCAGGGTAGGAGGCTCTCCTGCTAACGTGTGTCACCTACAGCACCCAGTAGGTCCTCCCCTGTGGGACTCTCTTCTGCAAGCACATTGGGCTGTCTCCATACCTGTACTTGTGCTGTGACAGGAAGAGCCAGACAGGTTTCTTTGATTTTGATTGACCCAAGAGCCCTCCTGTAACAAACGTGCTCCAGGAGACCATGAAAGGTGTGGCTGTCTGGGATTCTGTGGTGACAAACCTAAGCATCCGAGCAAGCTGGGGCTATTCCTGCAAACTCCATCCTGAACGCTGTCACTCTAGAAGCAGCTGCTGCTTTGAACACCAGCCCACCCTCCTTCCCAAGAGTCTCTATGGAGTTGGCCCCTTGTGTTTCCTTTACCAGTCATGCCATACTGTTTGGGAAGTCATCTCTGAAGTCTAACCACCTTCCTTCTTGCTTCAGTTTGGACAGATTGTTATTATTGTCTCTGCCCTGGCTAGAATGGGGGGCATAATCTGAGCCTTGTTCCCTTGTCCAGTGTGGCTGACCCTTGACCTCTTCCTTCCTCCTCCCTTTGTTTTGGGATTCAGAAAACTGCTTGTCACAGACAATTTATTTTTTATTAAAAAAGATATAAGCTTTAAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028064:ENSMUST00000029700:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.471 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(36.8=61.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTTGGAAGCAGGACATGG
R:
GGCTGGTCCTGGCTGTCTA
Band lengths:
342-892
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types