MmuINT0040178 @ mm9
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137660164-137662458:-
Coord C1 exon
chrX:137662342-137662458
Coord A exon
chrX:137660233-137662341
Coord C2 exon
chrX:137660164-137660232
Length
2109 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
GTTTTTCATATTTTATCCAGGGG
3' ss Score
6.66
Exon sequences
Seq C1 exon
GGCCACCCTGGACAGCCAGGTCCAAGAGGTCCACCTGGCCCAGATGGCTGTAATGGAACTCAAGGAGCTGTTGGATTTCCAGGCCCTGATGGCTACCCTGGGATTTTAGGACCACCT
Seq A exon
GTATGTTACCAGATCTTTGCACCTTAATGCAAATGCACCTTCAAATGTGTTTTTGTTTGTTTGCTTGTTTGTTTATCTTGAAACACCATTAAGGCCTTGTAGACAGCCACTGTACTACCTTGCCCAATGCAAGAGTTTATACGGATGGCACCATAACAGCAAAACTCTTTAAAAGTGCCAGTTGAGGGGTGCACATGTTAAATGACTTTAGGTTACTTTCTAATGCTACCTTGGGAATTGTCAAGATTGTTAAAACAAACAAATAAATAATAGTTATAGCACATTTCCGAGCAAAGCATGCACTTGAGCTATTTGGCATTTTGCCTATCAGGTAACATTGGGATATTCCAGGGCTGGAGAGATGGCTAGCGGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCTAGCAACCACATAGTGGCTCACAACCATCTGTAATGAGATCTGATGCCCTCTTCTGGGGTGTCTGAAGACAGAGATGGTGTACTCACATATATAAAATAAATAAAATCTTTAATAATGGGAGAGGATATTCTTGGAAGACCTTCATGTGATCATATGCATATTAACCAGGACCTAAAGGCATGATGAACTTGGTTTATACCAATAGTTTCCTGACTTGAAGAATAACACATTTCAAGCTCACTATTCATCTAATTTGGAAAAACCTAAATCTATAAGAGTTGTCATGTGAGGCCATTTGAAACTAGAAATCATACAACCAATTATACAGATCTCATAGTTCTCTGAGTAGCCTTCAATGACCAAGTTGTGGAGTATAAGAATACATGCAAAAAATGACACAGAGGATAGGCAGAATACAAGCCCCAAACTGCCCTAAAGGACCCTGCCATCAATGGTCCAGACCAATAAACAGCAGAGAGATAACAGGGAAAGCTATAGTCCTAAATAATCTACACAAGTCTTAAAGGCTCCTTAATGCTGCCATGGCAACAGAAAGGGGAAGAAAATAGACAATGAAGCCAGCAAAGGAGAGTTCCACCCCAACAAATGGAATAAAGACCTTGAAGTAGCAGACATCCTCTGAAAGAGAGAACCCCAGAGTGGAAACCTAAACCCAGCCTGAAACTTTACCTTAAGTTTTAATAGAAATGTGGGCATATGTTTTTACTAAGTTGAACCTCACCTCCTGCTGAATATCCATTCAGTAAGTCCATTTGAAACTTCTATGAAAGAAAATGGGGAACACATAAATAAGGGGAAGCAGACAATATTCAGAAACTGATTTGCATGTCTAGGCGCTTGTTTTACTAGAAGTACAGTAGTCCCCTTGAACTTGAGGAATCCATCATCAATCAACAATGTATTCTCCAAAGTGTACCCTTAATACTACCTAATACTAATCCTGACTTCTCCTTAGATGCCACCATTTGCTACTAAGACAGGAAACAAAAAGAAATCTGATTGAAAGACTGGAATCAGGTATATTGACTGATTTCCATGATAATGAGACACACCAGCTTTTTCAAAGGTTTGAAGCTGAAATTGTGTTGTAGAAACACGAGATGAAGTTGGTGTCATAGTTGTTTTAGACCCATGGCCTACGTGTTGGCCCCCAAAAGCACCTGTCCTCTAGCCTGTTTTTACATCTTAAAAATAAATAACAAGAAAAATATATGACAGACCCCAGATTTGACTCACAAAACTTTAATGATCTAGAATCGTAGAAACTTTTGTTGACCTTTGACCTAGATAAAGATCCAGTTAGTGAGGTAAGGGGTAGAGTTTTACCTAAACCAGTGTTCTCCATAGATAGAAAGTCTGCTGCAGTCTAACCCTCATCATTTCACAGACCCCTGGCATAGAGACAGAAGAATGGCACCCAGCTTCAAGACGACCTCTTTAGAGGTTAGGCTATTACCTTTAACACAGCCAAGTTTTCCACAGCAAAAGACACATAATTTCAGGTTCCCATTGCCAAATCCTCTATCTAATTAGGTAATATTGCTATGAAAACTCTGCGTGGGTAAGTGGAGTTTTGTTTTTCATTTGTTTTGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCAGGGATTTTCTCACAGGTTTTTCATATTTTATCCAG
Seq C2 exon
GGGCTGCCTGGTCACAAAGGTGCCAAAGGAGAGCCTGTTCCTTTTCAAGGCAGCATTACAGGAATAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:6
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=PD(2.9=5.1),PF0139113=Collagen=FE(61.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(21.0=56.5),PF0139113=Collagen=PU(10.3=26.1)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: