MmuINT0040135 @ mm10
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:141571966-141576041:+
Coord C1 exon
chrX:141571966-141572028
Coord A exon
chrX:141572029-141575987
Coord C2 exon
chrX:141575988-141576041
Length
3959 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTTCCTTTTTAACTCCCAGGGA
3' ss Score
9.7
Exon sequences
Seq C1 exon
GGGATGCCAGGCCATGATGGGGCTCCAGGACCTCAAGGTATCCCTGGATGCAATGGAACCAAG
Seq A exon
GTGAGGTTGGTTTTTTTTTTTTTTCAACTTAATTGTAAACAGATTGTTGATTAAAATCTAAAAAGAGACAGGGTCATTTTGTGTCTAAGACAACATTTTCAGTATATTAAATTTCAGTAATTTATTTAAACCTGTTTAACTAGTGAGGATACTGAATTGGGTTAGGGGGTATTTTAAAAGTCTTTGTGTAAAGTATTATAAATATTAAAAATGGATTAAGACTTGTGTGTTTCACATACTATAGAAGTTGTTATGGGTAATACTTGGTAATATCTTACTAATTTTGATTTTTAAAATACGTGCTATTTAAAATTTTGAATACTTCATGTTTTAAGCTTAAAAAAATTGTATGTTATTGATGCCGTGGAGGAAGAAACCGATGTATGCCACCGAGCACACATGGGGTTCAGAGGACAGCTTGTGGGTATTTAGCTCTTTCTACCTTGTGGACTATGGGTATCAAATTCAGATTGTCTGCACTTTGGCAACAGACACCTTTATCTACTGAACCATCTCAGTGATTTGATTCATGCTTTATTTTTTAACTTCCTTAACTGTCACTGTGAAAAATACAATTTTTTCATCAACAAAAATGGTGCACTTAACAATTTAAAAACCCCAAAGCTTTAGATAATGGTACTTTTCTTGTTTGGAGTCAACAATTTAACATTAAGACATAGCAATACATAATGAGGAAAATGTTCTTATTATAAAATGATATTTTATAGCATTTGATTTTTTTATTTCTTGTTTTTTCTTTTCTTAAGTAAATGCACCATTACTTTATGTTTATCCTTTTAGCATTTTATGTTTTGTGCATAAGATTCTACAAAACTAGATCTATACTATATTTTAAAATTAATGTCATATCCCAGATTTTTACATTAGGGTATACACTTTAGTTAACTTCCTGCAATACAAGGAACATGTTTTCTGAGATTTTAAAAACATACATAAATTGAACATATTACTTTTAAACCCAGTATTTCTCAGGTCTCTGTAACCCTTGCCAACAATAATATTTTTTTTTTCTTAACACAGAGTCCCACTATGTAGCTCTGGCTAGCCTCAGACTCACAGAAATTCACCGGGCCTCTATCTCCCAAGTTCTGGGAACTAAATGTGCACCATGTTTGTCGCAACAATTATATATATATATTTTGAGACAGGGTTTCTCTATATAGCTCTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCTGAGTGCTGGGATTAAAGGCATGCACCACCATGCCCGGCATAATTTTTTTAATGTTTAGATTTTTTACATTTTTATTAGATATCTTCTTCATTTACATTTCAAATGCTATCCCCAAAGCCCCCTATACCCTCCCCCCCTGCCCTGCTCCCCAACCCACCCACTCCTGCTTCCTGGCCCTGGCATTCCCCTGTACTGGGGCATATGATCTTTGTAATACCAAAGGCCTATTGATGGGAGTCTAGGCCATCCTCTGCTACATATTCAACTAGAGACACAGCTCTGGGGAGTACTGGTTAGTGAAACATTTACACAATGGAGTACTACTCAGCTATTAAAAACAATGAATTCATGAAATTCTTAGGCAAATGGATGCATCTGGAGGATATCATCCTGAGTGAGGTAACCCAATCACAAAAGAACACACATGGTATGCACTCACTGATAAGTGTATATTAGCCCAGAAACTTAGAATATCCAAGATACAATTTGCAAAACACATGAAACTTCGCTCCTTCTTAGAATGGGGAACAAAATTTCCATGGAAAGAGTTACAGAGACAAAGTTTGGAGCTGAGACAGAAGGAAAGACCATCCAGAGACTGCCATACCCTGGGATCCATCCCATATACAACCACCAAACCCAGACACTATTGCAAATGCCAGAAAGATTTTGCTGACAGGACCCTGATATAGCTATCTCTTGTGAGTCTATGCCAATGCCTGACAAATACAGAAGTGGATGCTCACAGTCATCTATCGGATGGAACACAGGGCCCCTAACAAAGGAGCTAGAGAAAGTACCCAAGAAGCTAAAGGGGTCTGCAACCCTATAATGTGTAGATCATTAAGGCAAATATCTGGAATTGAGAAATTTATTTATGTTCTTCATTCTAGCTGAGACAGTCTTTGATGGTTGGACCAATAGGAATTTTGTTTGTATAACACATTTCATAAGAAAGTGAACTATGGTGATGGAGTAATATACAATTGATGAATAAAGAGATAGGCTGTTAAAGGCTTTGAAATAAAAAAAAAGAAAGTGAACTATTTTGTTCCTATTCTGGTGGCATAGCTATGTTTTACTTTGTTCCTTTTCTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGGTATGTATGCATGCATGTGTGTTTGCTAGCATACCTTTTGCAACAAGAAAACTAGTATTCAAAGTTTTAAATAAAGAAACCAAATGCACATGCAGATATATTTATGGTGAAAGAGATATTTTTCACAAAGTGGTCTTTTCATATATCTAACAATTAATTTATGTTTTAGGGCATCATTTATGGAATAAGTTTTATATAAATTAAGTAATTTTATCGTACATGGTGACTGGTTAGACTTTTTTTACCCTTCTCACTAGGTATGTAAAATTTGATTCCTAATGTTGCATCCACAATGTATGGATTCTTTTCTAATGTCATTGGACCTAGTTTATTTTTTATTAGGTATTTTCTTCATTTATATTTCCAGTGCTATCCCAAAAGTCCCCCATACCCTCCCCCTCGCTCCCCTACACACCCACTCCCACTTCTTGGCCCTGGCATTCCCCTGCACTGAGGCATATAAAGTTTGCATGAACAATGAGCCTCTCTTTCCACTGATGGCTGAGTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGGTATTTTCTCTAGCTCTTCCATTGGGAGCCCTGTGATCTATCCAATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAATCTCACAAGAGACAGCTACATCTGGGTCCTTTCGATAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGAAGCTGATTATGGGATGGATCTCCGGATATGGCAGTCTGTAGATTCATTGGACCTACTTTGTCCATCTATAAAAGGTGATTCAGAGAAGGCCATTGCATAGTGATTCAAAAGCACAGTGGGGTAGTAATTTTGCCCCTTTAAGCCTCTGACATGTTTGTTTCTAGAATTGCTATAGCATACATAGGCATTTGGAAAGAATTTGAATTAATTTTCTTCTATCTCAATTTTAACTTGTTTTCAAACCAAATGTCTATGTTCCTACTTTGCAATAGTGAATGAAAAAGATTGGGTACCTAAGAAATCTAATGGCCTGCAATTTCTAAAACCGTTGTTACTGTATTCTTGGTGCTATCACTAGCTTTATTCCTTGCCATGTTTTACATTTTGAAAAAAAATTGAAATAGTTTACAATAAGAGGAAAGTGAAATGGTAAGTTTTTAATAAGAATTTGTACAGTACCTGATCAGGAACTTGCAGCAAATCATTAACAATTAAATGTGATGGTTATTGGAAATCTGTGGTGTGATGGGCTCAAAGTAGATTTTTCAAAAGAATATGACAGTGAGACTGTTTTCTCCTTAGATTTGGTTGGGGTAGATGAGTACGAATAAGAGTGTTCGGCTTGGTAGGTTGAATTGCCACAGACAGTTGATTCTGAAGTTATTGGAAAGGGGATGCTAATGACATTTTGGTGATCTGGTATGCATTTGTCGTACAAATTTTCACTGTTTCTTTTTTCTCTACACTCTTCCTTTTTAACTCCCAG
Seq C2 exon
GGAGAACGTGGATTTCCAGGCAGTCCGGGCTTTCCTGGTTTACAAGGTCCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274:ENSMUST00000112931:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(13.6=57.1),PF0139113=Collagen=FE(31.2=100),PF0139113=Collagen=FE(31.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(14.1=50.0),PF0139113=Collagen=FE(27.0=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