MmuINT0039169 @ mm10
Intron Retention
Gene
ENSMUSG00000040690 | Col16a1
Description
collagen, type XVI, alpha 1 [Source:MGI Symbol;Acc:MGI:1095396]
Coordinates
chr4:130073240-130077052:+
Coord C1 exon
chr4:130073240-130073293
Coord A exon
chr4:130073294-130076998
Coord C2 exon
chr4:130076999-130077052
Length
3705 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
TTGTTTCTTTTCTGCTTCAGGGA
3' ss Score
10.95
Exon sequences
Seq C1 exon
GGTCCCCCAGGTGTCCCCGGACCACCAGGTCCCCCCGGAATGCCTGGATTGCAG
Seq A exon
GTAAAAGGACTAGAGACTAGAAGAGAGTCTAGAGATTGGGGGGGGGGGACAGGAACCAAGCAGTTGTTGGGGCTCCTCCATGCTGGACCCAAGTGCACTGGTTCCTCTATGCACACATCTGCTGTGATTTCTTAGTGCCATGGCTTCCTCGCATGGTGTGCTGGGCTCACAGATCCCTCGTTTTGGCTTGTGGACTCCCAGCCTCATTCTGAGGAACGTCCTATCATGTTTTAGCCCCGGAGACCCACTAATAGAATCCACACCAGGCCTGGCAAGAACCCAGGCTCTGAGGCCAAGCACTATACTGGTCCAGAGTGCACTGTTGGAACAGCAGTCAGTATGTGTTGGTGTGACATGCATTTGTGCCTATGTGATCTTTCCCATGTATGGTTTTAGATGCTGGGATATAGTGGTGGATCAAGCATTAGTAGCCCTGCAAGAGAGGCAGACAATAAGTAATATCTAGACTAAGGGGATGATAAGGCTGGGTATAGGGATGGATGGTGGGAAAATAGGGAAGATACTTGTGAAAAATATTAAAGAATAATGGGTGCCATTTAGAGCTGGGAAGACGCCTCGTCAGTAACGTGCTCACCATACAAGCTTAAAGACCTTGAATTCAGATCCCTTGCTCCCACATAAAAAGCCAGGCACAATGGCCTGCGCCTGTAACTCCAGTGCTGGGGAGGCAGAGACAGGTGGATGGCTGCGTGGGGCTGCCTGGCCAGCCAGTCTAAGTGAATAGGTAAGCTGCAGCTTCAGCGAGAAACCCTGTCTCAGATGTTAAGGTGGAAAGCCGATGAGATCGCTCCAGCAATAAAGGCGCTCGCTCACATGCAGGCCTGCTGACCTGGCTCCCATCCCCACATCCCACAAGGTAGAAGGAGAGAAGGAAACCCTCAGCTGTCCTCTGACCTGTCCACGCTTGCTGTGTCATTGTGTGACACACACAGAGGCATACACTCACATACACACAGTACACACGCGCACACTCACTCATACACGTATACACACACGAGCACATACATGCACACACACACATTAAATTAAAATAAGGTGGAGAGCAACTGAGGAAGACACCCAGTGTTAACATCTGGTCTCAACGTGCAAATGCATACACATACATGCGCATGACTTGCACACACATGTGCATGTACACCTGAACATATATGCACATGCAAATCAAAGGTGACATTTGGATCAAGATGTAAAGGAAATGCAAGTGAACCTGTTGAGGAGAAAACATGTCTGGGGAGGAGCACACGTGGGGAGGAGCACCTCTGGGGAGGAGCACCTCTGGGGAGATGCACCCCTAGCAGGGAAAGCAGCAGGTGCAAAGGCCTAGAAGTGAGAATGTCCATGGTGTCCTCAGGAAATAGCACAGAGGCCAGAGATAGGAAGGAAGGAATATCAGGAGGAGCCGAGATCTGTGTCACACTTCCAGCCTCAGTTTGAGTCTCCTTTCTGCCATGTGCTCTGTGACGCTGGGCAAGTCACTTAACCTCGCGATGTCTGCATACCTTTATCTATGAAATACAGATAATTATAGCACCTGCCTCAGTGGCTTCTTGCGAGTATTGAATAAGCTTGTGTGTTCAGTGCGTGTGAAATCTTTCCTGGCACACCGTGAATGCCCGGAGGGTTAGCTGTCCCCACAATGTTTCATGTGGGGAACTATGTCACAACTTGGACAGCTTAAGCTCTGAGAGGTGAGGTGTCTTGTCCCAGGTCACCCAGCCAGGTATTAAAGCCTCGGGGCTTTCCCTAGCAGAGCCCTTCCTCCTTCTTCCTCTGCATTTCAGGACAGTCCTCAGGGGAGGGGTCACTCCCCAGGAACCAGAGCCCACACCACACACTTGGCAGTCCCTGCACGGGATGAAAGAGTCCAAGCTTCCTGTGCAGTGCCAGCAGCAGCCAGTGATCTGTCAGCAGGGGGCACGGAGTTTGCTTGGGGAGGCTGAGTCATTTCAAAGTGACCCATTAACCAGGGAGAGCTGGCGTAGTGTGTGAACTGTGCCAAGCCACACTGGGGGAACGAGGGCAGGGAAAAAAAAGTGCTGAGTGTAATCCCAGGACCCAGAATCGGATCTGACGCCAGTGCCCGCAACCAACCCGGGGCTGCCACAGGCACCTGCCCTGTGCCAGGCTTCTCTGTGCAGGGGGGTGGAGCCAGGGATGGATGGCTGACACTTGTTTGCTGGAGGCTGCATCCTTCCAACGCCTTCACACGGCATTTGTCTTGATCCATTTCCCAGATGAGGTGCCTGAGACACAGAGGCTAAGAAATGTGCCCGAGGTTTTTAACAACTGGCAGGTAGTAGTCAAACCTGGCTGCATCCCCTCCTTGTACAGGAGAACACAGATATGTAATTCAATCAGGCTAAGAATCACACTCTCAGGCTTGAGCTAACACCGCAGCACTGGAGAGTGGAACAATGCAGTAACGGCTGGGGTGTCGCTCAGTTGGTAGGGTGCTTGACTAGCATACAAAACTTGAGCGAGGTGGCACATGCCTGTAATCCCAGCCCCCAGGCAGTAGAGGCAGTGAGGTCAGAAGTTTAAGACCATCCTCAGATACATAGTGAGTGTAAGGCCGTTCAGGACTGCATGAGACCAATTATCTAAACAAAAATATTCAAAGCATTACCCATGTGTCAGGTACGATTCTTCTAGATCTTGTGGGTCCCAATGGGTACTAGAGGAGGCTGGGTGGTGACCCAGCAGTGGGAGCATCTACTGTAGATAGGAAAGGGGCTGCTCAGGGGCAGCTGACCCGTTCCAGTGCCAGAAGTTGGGTCTTGAAGGGAGGTCAGATCTCAGAGCAGGCCAAGGAAATCCTGTACCAGGAAGAGCAGGCTGTGCAGCAATGCGTTCATTCAACACATATTTAACGTGCGCCGCCGCCTCCTCGTTAGGTGCTGGGGATTTAAATCCGAACACCCTCCCTTCTTCAGCAGAGTATTTAATATGCAAATGTGCAATGTGAACATGCAAGGAAGCTAGAGGCTGGGTGGCAAACTCTTAACAGGAGTGTCCCCGCACATCCTACATCGGGGCTCTGTGCTGTGTCCCTCACAGCAGCATGACTTCCTCGAAGCCATCTCTGCATGATGACCGTCTTACAGAGAAGGAAACCGAGGCACAGCGCTGGGCTCATACTCTTCCAAAAGTTACTTGGGTGGTGAGGACTTGCACCTAGATGCTCCGATTGGCAAGCATCCAATACTGCAGGGACATCTTTCAAGGGATGGGGCACAAGTAGGGGATGAAGAAAGGTTGGGGAGCCAGTGGTCCTCTCCAGTAGTCCCAGTGACACATCTGTATCACTCAGCCTATGACCTTCTCTGAGTCCCTTTGTTTCCAGGACTGCAACAAATCGCTTGTAGCCTCCAGGAGACTACAATGGTGATTAATGAGAAAGTACGGGAAAGCAGCTTAGAATAGCCCTCAGCAGTCACCCTATTGAAGACCCCCTGTCTAGCTTCTGACCTGCTGCACAAGGAAATGCTCCCAGTGGAACTACTTTTAAGGACCATCCACTTCTGTGCCTCCTTGGCTCCCGCAGCCCCCAGCCGTGGGAGACCTTGAGGCCTAGAGTAGTCAGAGCTACCACCCATGCAAGAGCGGCTGACAGGTGGCAGGGCTGTGAGCCCTAGCAAGGAGATCACTAAGAGTCTCTGAGCTCTTGTTTCTTTTCTGCTTCAG
Seq C2 exon
GGAGTGCCTGGACACAATGGTTTGCCAGGACAGCCCGGGCTCACTGCCGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040690:ENSMUST00000044565:42
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=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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
- 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