MmuINT0141152 @ mm10
Intron Retention
Gene
ENSMUSG00000021451 | Sema4d
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D [Source:MGI Symbol;Acc:MGI:109244]
Coordinates
chr13:51720506-51722380:-
Coord C1 exon
chr13:51722318-51722380
Coord A exon
chr13:51720605-51722317
Coord C2 exon
chr13:51720506-51720604
Length
1713 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
ATGGGGTGTTTCCCTTGCAGACG
3' ss Score
10.13
Exon sequences
Seq C1 exon
GTATATTGGAAGGTCTCTGAAGACAAAAAATCCAAGTGTGCAGAGAAGGGGAAATCAAAGCAG
Seq A exon
GTAATTGACCGCACGTACAAAGAGCCCACGCACACAGTTCGCAGTTATTTGGATCTTTTCCAGTAGCAGTCTTCTGCATGCCTACCTGGTATCACGTGAGTCTGGTGGGCTCGGTCCTGCTGTCTCAACCCTACCAGCATCAGGATTGGTGCTCTCAGGCCAGTGCCCTGCATCCTCCGCACTGGAGAAGCCTGTTCTCACGGCTTGGCATTATGACTACAGGATGTTGTTTCTGCTGCCCACTAGTACCTGGTGTAGAATTGGCCTCCCCTATATGTTTCTGGCCTTCTTGAACCAGCTGAGGCCTAAGAGGTGTTGGGGATTTGATGGGATTTGTTATTGTTGGGTTTATTTTTTGTTGTTGTTGGGTTTTGTTTTTTTGTGGGTTGTTTTTTTTTTTTTTCCTGTATTTTGTTGTCAGATACCAGTATGCGCACTCAGGGAGACTGAGCCTTGTATCCTTTTTCTCAGGAGCTCTGAGTACCCTCTTGTGCCTGCCCACCTGGTGTCCCACCAGTGTCCCAGATGTTTTTAGATCACGAATGTTTTTAGATCACAGGAGCCAGGTTGTCCCCAATATTGGTCATGGTGGCTCAGCAGTGGCAGAGTTTATCAGCTGTTAGCTGATTTCAGAAACAGGGATTAAAACAACCACTAGGAGCCGGGCGTGGTGGTACACACCTTTAATCCCAGCACTCTGGAGGCAGAGGCAGGCGGATTTCTGATTTCGAGGCCAGCCTAGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACAGAGAGAAACCCTGTCTCGGAAAACAAAAACAAAAACCAACCACTAGGTTAAACTTTCTTGGCTAAATGGTAACTGAACACTTTCCCCGTCTTACTGGTCTCTAACTGTAGTGTTCACTCAGGACCCAAGGCAGGCAGGCATTACGATAGGCTCCCTGCTGCAGGAAATCTGTGTAGCGGAGTGAGCTGATGCCTTGCACCACTGGATGTGGGGACCCACAGTGACCTTGGCATGGAGCCCTCCTGTGATACCCTGTCCATTTGAGGGTTGTTGGGGAAAAAAGCAACAACAACAACAACAACAACAAAAACCCCTTTCCCAACTTGAGATAATTTCAGGCCATAGCCCATAGACTCTAAGTGCTGTTCTCCTGAAATAGCACATGGGCTCCAAATTGCCGTCTTTGTTTTCCCACTGGGCCCTCAGGGATACACAGCTGGCTGTACTCTTGGGTCCAGCCTCTCTCTCAGTTCCTGCTAGTCGCTATTTCTAGTTCTGTGCTGGTGGCAAGAGTATAGGGTGGGGTCCCCAGGAAGGTAGAAGGAGCCTGTACAATGTCTGTTTTGGCAATATGGGCCCCCAAAATGAACGGTGTGTGTTCAGCAAGGGTAAATACATTGCCATCTGTAGTGGGCTCCCCAGTACAATTTGAGGTCAGCTCTGGTTTGGTCTTTGCTTTGCTTGGTCACCAGATACAGGCTGGCCATCTACTTAGGGATAGAGCTAAAGTCATGCCTGGCACCTGCACTGCATGTGGACCACAGAGATAAAGTTTCCGTTGCAGAGCCTGGCTCATGGTGCAGTGTGCCCCCTCTATGGGCATAGACAGACCAAACCTGAGCAGAGGAGAGAACAAGGCAGCAAATGACTGGCCTTTACCATGTGGATACAAGGGTTCTTTGATGGGTGCCTGTTAATGGGGTGTTTCCCTTGCAG
Seq C2 exon
ACGGAATGCCTAAACTACATTCGAGTACTACAGCCACTAAGCAGCACTTCCCTCTATGTGTGTGGGACCAATGCGTTCCAGCCCACCTGTGACCACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451:ENSMUST00000110040:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(20.6=100)
A:
NA
C2:
PF0140314=Sema=FE(33.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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