MmuINT0040088 @ mm9
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:138013215-138015165:+
Coord C1 exon
chrX:138013215-138013295
Coord A exon
chrX:138013296-138015102
Coord C2 exon
chrX:138015103-138015165
Length
1807 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
CTTTACTCCATTTATAACAGGGC
3' ss Score
6.79
Exon sequences
Seq C1 exon
GGGGAACCAGGCAGTATAATCATGTCACCACTGCCAGGACCAAAGGGTAATCAAGGATACCCAGGTCCTCCTGGAATACAA
Seq A exon
GTAAGAGTATGGGGAATTTTTTCTTTATTACATGATTAAAACATAGGATCATATGAGTCCTGACCTTCTATACTCACTGTTGCTGTTTTAGTTATACAAATTATCACCTGAAGTTCTTAAGGTCTCAATGCATTCCTTCTATTTTAAAGTAAAAGTTTTTACAAGGCATATTTGTTTTCTTTTATCTATGTATCCAGTGTCTGTGGGTATTTGTGTATGTGGCAACAGAAGTTTGCATCAAAAATAATTTCTGACATTCTTCTTCTGCTATAGGTAGCAGTAGGGTTGACCATAAATGTTTTTTAACAAATAAAATTATCGATCTCTCTTTTAAGATGTTAAAATTGCCATTTATAACAGTATCAATTATGCATGATATCTGAGCAGACACTGAAGGTTGAAGGAATGCAATTTATGCATGGTAAACATCAAATGTAATCTTACAAAAAGATTGTGTTAGTTTATAGATAATATACAGAGACAGTAATGACTTTTGAGTATTTATAGATGAGGAAGTTCATTATAGTTTATGAAAATCAATCCCTTTATCAAAAATACAAATCAGGAGGTTTTACTGTTTGATCACAAAGATACAATTTTGGAGATTTTTTTCATTTGTTCATTTTTTATTCTTTACCTGACATTACTAGTCATAATCTCTTAAGTTCATTCAAATATTCTCCTTAATCATACATATAATTTTTAATGAATATTTAAGATAAAGTATAACAGATCATATGCAGAATATATGCTGAGATAACACAAAATGAACACCTAGGAACACTACTAAACCCAACAGAAAGTTACAAATAATTTTGAATCAATACAATGTTACCTGGAAGCCACAGCCTTCTTGATTGCCTCAATATATAACTAGGAGCCTGAGCAAACTGTTTAAAGTTGCTTTATTCCCTCAACTGTATCAGCTTTCCTTTACAGTATGTGATAGTCACGTAATCTGCTGCAATGCATCTGTTTTCCTTGGCTTGTTAAGGTTCATTCGTATTGTTTTGCTATGGTTCATTTTTTTTCTTTTTTCATTATGTATTTATCATGTTTTTGTCTATCATTGTAGAACATAATCTTGCTGAAAGCTGTACCCCATCTCTCTTATTGAGTTACCTTTTAAGCTACTTAGCCCTTCTATTTGTACAATTTTTAAGCCCTGATAGTATTGCAGGGTTATAGACTTATGAAAATAACTTAACTTGCATACATTTATTTCTTTATATGATGAGGTAAAGGGTTGAGTTTAGGGATTTTGTTTTTCATACTTCTTTCCTCATTAAAATTGATAAAATATAGTCTTTAAAATATATTGTTTACTGGTTTCCTTTCTTAATAACATGAGAAAATAGAATTAATGATTTCTCTGTTTTTGAGGATTTTTTCCTAGGGGGGAGGGCGAGAGAGGTGACTAAGCGATATCTATCACCCTGAGAACCAGTGAGTTTATTAGACTTACTTAGAATTGACAATAAGTTACTAAGAGGAGTGCAAGTGACCTAAAAGCCACACTGAAAAGTCTTTACCCAGGATGTAGCAGGGCTTTCCTGAAGCCATGTAGGGAGCTCTCCCTTTCTCTAGGCTTCCCAGTCCCTGACCCTAGATCATCCATAACATCTTGAGGCTTTGTATGACTAAGGCCTAAATATAAAATCGGCTGGGATGGCTCTGTCCATATCCTCCTTTTGTTAAGGAATGTAACATTTAATCTGTCCCACTGTGATCATGAAGACAGCACTTGTTTAACTTAGAGCAGAAGCCCCACATTCTAACATACTTTTCTTTACTCCATTTATAACAG
Seq C2 exon
GGCCCACCTGGTCCCAAGGGTATATCAGGGCCAAGTGGTCCTCCAGGACCACCAGGTTTAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274-Col4a5:NM_007736:10
Average complexity
IR-S
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=PU(28.8=63.0)
A:
NA
C2:
PF0139113=Collagen=FE(33.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: