MmuINT0040157 @ mm10
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:141190222-141192217:-
Coord C1 exon
chrX:141192056-141192217
Coord A exon
chrX:141190393-141192055
Coord C2 exon
chrX:141190222-141190392
Length
1663 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
CCTCTTCTATAACCATTCAGGGC
3' ss Score
7.55
Exon sequences
Seq C1 exon
GTTTGAATGGGAAACCTGGTATGCTAGGCCCCAAGGGTGAGCGGGGCAACCCTGGAACATCAGGACCACCAGGACAGCCAGGACCCTCAGGGTCTACTGACCCATTTGGCATCAAGGGCACATCTGGATTCCCAGGAGCACCAGGCCTTCCAGGCATCTCAG
Seq A exon
GTAAATCCATTGAAGGAAGAATCCTGACTTGGCAGGGCCTTACTTAGACAAAGGCACCCCGGGGACTAAGAGTGGCAGTATGATATGCTCAGCACCTAGGATATTTGACTTTCCTAATCTCTCTAGTTTCAAATCCCAGATCATCCTGGCTGGGCCAGACCAGAACACATTGCTACTGTTTAACTTCTGATCCATGACAACAAATCTCTGTCACCTCCCTTTTCCAGGGCCTCCTACATCCTTTTGGTGTTTTTGGCCTGCTGCTGGCCTTTTTCTATTAAAGAAATCACCCTGTGTTGAATGGTGTTAAACCCTCGCTGTGGCTATGTTAAGCCTGCTTTGAGCTACAGAGAAACTGGAGCTGATTGTGACCTCTTCCCTCCCCCACCAGTAGCCTGCCTGTCAGGAGAAAATGCCTCTGAGGGTCCATAGGCAAATAGTGGCTTTCACTAAGCAATGAGGACTGACACCCACTGGTTTCAGCCTAACATTTGCAGTTCACCTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTATACCATCATCCTTACTCTGACACCTAGACTGCATCACTGACCAAGTGACTGAAGCTGGGTTATTTGCAGAGCTGTTAATATCCCTTTTATTTCCTCTATCCTGTTTCTGGGGCCTTCATATAAGTTGCTGAGGTGAAGGTTAAAAACAACAACAACAACAGCCCACAAGCTCACTGACTAAGACTCCCCATGGGGAATTGTGTGATTGTCTGCTATAACAAACCTTGCTTACAAGGCCAGAGATCCCTGAACCGCTGCTATAAGGTTTGTTCCCACTGCATTCCCTTCTCCTGTTGCAGACTTATCCTCATTGCTTCCTATTAGATTCCTGCGGCTCACAGCTACTTGATGCTTTTCATTTCATGGAAAGCTAAGTCAGCCATTCATTGAGGTCCTTGGGAACCCAAATACTTCTGTCCTCAGTGATGTAAGCCTTTGGATTTTTCATTTCCTTGCTTTGTACCTGGACATTCAACTTCGGCAGCAGCTCAGGAGGTTAATCCCATTGACCAACTTCAAGCCCTGGTGAAAGAAGACTCAGAATACCTAAGAGACCAAATGGGCCTTGGGGGTTTCTACAATACTTGGCACTAGGGGGTCTTTCAAACCTAATGCCAAAGAACTGGCTGATTTAACTGCTTGTTTGAGGGATTAAAAGGGCAACCCTAGATGCAAGACTCCCTGGAAAGCCAGAACAACAGTTCAGATTTAACCTCTATTTCATGAATTGGCTCAGGAAACAACCATTGGAACTTGATTCAGGGTTGAAGTCCCAGGGAAACTAGAGCCCACTTGCCACCCTGGCTTCCCAGAGCTCCATTTAGAGGCTCCTCTGTGAACCACATTCATAAAGGAAGAAGTTATAATTACAAGGTACTTGCTTTTCCTACCCACCACTGTGCCATGCTGGAAGTGATGAGCATTTAGGGAGGTGCTCTGGGTGGTAGGTACTAATGCTCTGACCAACTCAGCACCAGGCTTCTTGGCATCTCTTTTTAGGTAGTGTTAAAGGACCGTGGACAAACCCCTCCTAGCCAGCCAAAGAGAACCTCTAGAAATAAACAGTGGCCCAAACCTGACCAGAGCCTGACTAAGCTGACCTGTGTCCTCTTCTATAACCATTCAG
Seq C2 exon
GGCACCCTGGAAAGAAAGGTCAAAGAGGAGACATAGGTCAGCCTGGATCAACTGGAAAAAGAGGTCTACCTGGGATAAAAGGCCTTCCTGGTCCTCAAGGGTCACCTGGCTTCCTGGGGAGCCCAGGTTTGTCAGGCGTCACTGGGTTGCCGGGCATCGAAGGCCAAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273:ENSMUST00000101205:27
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(47.5=52.7),PF0139113=Collagen=FE(76.1=100),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(41.2=60.3),PF0139113=Collagen=PU(65.9=93.1),PF0139113=Collagen=PU(4.5=5.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
GAAACCTGGTATGCTAGGCCC
R:
CTTCGATGCCCGGCAACC
Band lengths:
314-1977
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