MmuINT0141148 @ 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
chr13:51701246-51704996:-
Coord C1 exon
chr13:51704953-51704996
Coord A exon
chr13:51703532-51704952
Coord C2 exon
chr13:51701246-51703531
Length
1421 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CGTTTATTTTGATGTTCCAGATA
3' ss Score
8.5
Exon sequences
Seq C1 exon
GGGCTGGATTCAGGACATGAGCGGTGACACATCCTCATGCCTGG
Seq A exon
GTGAGTGGATCTCCTTTGCTTCCCACCCCTGGGCTGGCAAAGCTCCCGGGGCGTCAGTTCCATGGTTTTCCTGTGCGGTCTGTCTTCCTTTCTCCTCTCTGAACAGAAGTCAAGTGTCACGCAGCAGACCTGTGACCTCTCCTTGTGGTGAACCTGTGATCTTTCTCTGTCCCTTTGGTTACAGAAAGAGGGCTCAAAGGCACACAGGGTGTATCGGTTCACTGGAAAGCACACCCTGGCCCACACCATGCTCCTCTGTTCTGCTTAGCTGGGCCCCGTAAACAAAACTGGAGCCTGCTAGGAATGAGAGCGAAGGAGCCCTTGGGTATGACCAGATAGCCCTAGCCTAAAAACAATACTCAGGAACAGTGTGGGACAGTGTCATGCTTCAAGATGAAAATCCTACCCTAGAAAGAAGTGCCTTAAACGCTAAGGAGATGGCTCAGTTGGTAGGATCTGAGTTCGATCCCCAGAACCCATGTAACAGCTGGGCATTGGTGGTTCATGCTTGTGATCCTAGCCCCAAGGAGGGTGAGGCAGGTGGATCCCTGGAGCTTGCTAGCCTCACACAGCCTAGCCGACTTGGCAAGTACCAGACAAATGAGAGACTCCATCACAGAAAAAGACAAAGAGGGTAACTGCTATCTGAGGATGATACTCAGATTTCTGGCCTCTTTCTATATAAACACACATGTACGTACACACACACACACACACACACACACACACACACACAGAGCAAATGGCATCAGATTGCCTTCAGGCATGTGTAAATGTCACACAAATTTCATGTGTAGCTTTCAGTCCCCTTCCAAAGATAGTTGTCTCGTTTTATATATGCAAATATTTCCAAGCCCAAAGCATTTTTCATCTTCCGTATTTCAGACAAAAGACACAGTTGTGGTTAGTTCTGGTGTCCTCTTGGGGCACCCCCTCCTGATGGCTGGCCATCAGGAAACGGCTGTGACCAGAGGTAGGCATAGAATCTTGCCAGAATTCTAGTCTGCCTTCCCAGCCCCGTACCCCCTTCTCTGACTAGCCACATCAGAGTAAGAAGAGGGTCCCTGGTTGCTAGCTGGCCTGCTTTAGCCATTAGCAGAAGTATTTGTCAGCTGACTGGGTGCCACTGTGAGGGAGCTGAGCCGTGCCCAGCCCCTTCCTCAGCCTGCTGACCTTTCTCCAGGGCCAGGGTGAGAACAGAAATTCTCAGAGCTGTCGCCAGTTCCTTCAGTGTATGGAAGGGGGACGGGGTGGGGGCTGCTCTAGGGTCATGGATGTCTTTACCTTGGTCCTGAAGATTGCACCTGGCTCCAGTGGGTGGAAGTCTCATGCCGTCCTGTGGGTATTAACCTGTTTTTTGAAAGCAGTCGAGCGGTCAGACGGAGTTGTTGACGGTGAGCACGTTTATTTTGATGTTCCAG
Seq C2 exon
ATAAGAGTAAAGAAAGTTTCAACCAGCATTTTTTCAAGCACGGCGGCACAGCGGAACTCAAATGTTTCCAAAAGTCCAACCTAGCCCGGGTGGTATGGAAGTTCCAGAATGGCGAGTTGAAGGCCGCAAGTCCCAAGTACGGCTTTGTGGGCAGGAAGCACCTGCTCATCTTCAACCTGTCGGACGGAGACAGCGGCGTGTACCAGTGCCTGTCAGAGGAAAGGGTGAGGAATAAAACGGTCTCCCAGCTGCTGGCCAAGCACGTTCTGGAAGTGAAGATGGTACCTCGGACCCCCCCCTCACCTACCTCAGAGGATGCTCAGACAGAAGGTAGTAAGATCACATCCAAAATGCCGGTTGCATCTACCCAGGGGTCCTCTCCCCCTACCCCGGCTCTGTGGGCAACCTCCCCCAGAGCCGCCACCCTACCTCCCAAGTCCTCCTCCGGCACATCCTGTGAACCAAAGATGGTCATCAACACGGTCCCCCAGCTCCACTCAGAGAAGACGGTGTATCTCAAGTCCAGTGACAACCGCCTGCTCATGTCTCTCCTCCTCTTCATCTTTGTCCTCTTCCTCTGCCTCTTTTCCTACAACTGCTACAAGGGCTACCTGCCCGGACAGTGCTTAAAATTCCGCTCAGCCCTGCTGCTTGGAAAGAAAACACCCAAGTCAGACTTCTCTGACCTGGAGCAGAGTGTGAAGGAGACACTGGTCGAGCCTGGGAGCTTCTCCCAGCAGAACGGCGACCACCCCAAGCCAGCCCTGGATACGGGCTATGAAACGGAGCAGGACACCATCACCAGCAAAGTCCCCACGGATCGTGAGGACTCGCAACGGATCGATGAACTCTCTGCCCGGGACAAACCGTTTGATGTCAAGTGTGAACTGAAGTTTGCAGATTCGGATGCTGACGGGGACTGAGGCCAGCGTGTCCCAGCCCATGCCCCTCTGTCTTCGTGGAGAGTGTTGTGTTGAGCCCATTCAGTAGCCGAGTCTTGTCACTCTGTGCCAGCCTCAGTCCTGTGTCCCTTTTTCTCTTGGGTTGAGCCTGTGGCTCATCCCCTTTGTCCTTTTGGGAAGCAAGTATCTATTCCAGTCTCAAGTCCTGCAGTTGCTGGAGCGCTTACGCACCTGAGCCCTTTGTGTCCTGGGGGAGAGATGGCCACCTCCGTGGGCTGCGAAGAGCCACCCCTTCCTCTTCCGATTCTCCTAGCAGCCACTCAGAGATAATTTAATTCCAGATTGGAAACGCCCTTTTAGTTTATCAGATTGGTAACTTACATCCTGCTGCCCAGATGGCACGGACAGTTTTCTTTCACTTAATTATTATTTTTTTTTTAAGGATTTTCGCTCCTATTGTGTTGATGTCTTAGGTCATTTTCTTTTTTTCTTTCTCTTTTTTTATTACCAGAGGAGATGTTTTAATATTCATGAGAAGAGGAACATTTTCTAGATTTTTTTGTTGTTATATATTGAGATATAAAATATGGCTATGTTGCTTAAGATTCTCAGGGATAGACTTATTTTTGTTAACTTCATTCTTTCCTGCTGTTAGGAACATAGGCCTAAAATTGTCTCTTGAGTTTGCTCACCCTTTTGTTTTGGTAGGGTTTTTTTGTTGTTGCTGTTATTGTTTCTAGTTTTTAATCTTATTCATTTTGAAGGATTTTTCTTTCTGAACTTTTTAAATTTTTATATTTTCCTGCCATACATCTACAAAGTGGGTTTTGAGTGAGGGCAGGTGGCCCAGTGGCTTTGGGTGGCGACTGAGCTGGTCCCACGAGGGGAGGAGGGTTTATATACCCCATGACCCTGCGGCTTCTTGGCGCCTCCTGCCCATGAGGATCACATCCTGTCTCTCCTTGCTTCCATCTCTCATCACTGCCCTTGGACTTCCGCCTTGACTGTCCATGAAAGACAGAAATGGGTTGGGTAGTTGGGCTCCCAACCTCGGATGGTGACCGCAACATCCCGTGTGGGCGGCCGGCCGCTCCTGCAGCCCGACTCTCCTGCCAGTGTCTTTCAGGATGTCAACGGGTGGTACGATTCTGGCATTTGTTTCTCGCTCACCGTGTGTGGAACACTCATTCCATGTAGAGGGTGACGAACTCTGGATTCCCCCCCACCCCCACCCCGTGCCGTGTAGACACTCATCTTCTGCATGACATGATCTACCATTCGGTGTAAACATTTGTGTTTATAAGATTTACTTTGTTTTTATTTTTCTACTTGGAACTGTACACATTTGAAAAGTACCCAAATAAACCAGAAGCTTTATCGTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021451:ENSMUST00000110040:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.326
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGACACATCCTCATGCCTGG
R:
TGTCTGAGCATCCTCTGAGGT
Band lengths:
347-1768
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