MmuINT0039443 @ mm10
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4512361-4515254:+
Coord C1 exon
chr6:4512361-4512414
Coord A exon
chr6:4512415-4515209
Coord C2 exon
chr6:4515210-4515254
Length
2795 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGC
5' ss Score
7.42
3' ss Seq
TATGTGTATACTCTTTACAGGGT
3' ss Score
8.07
Exon sequences
Seq C1 exon
AACTTTGCTGCTCAGTATTCTGACAAAGGAGTTTCATCTGGCCCTGGACCAATG
Seq A exon
GTAGGCTTGTCTCCTTTTGTCCTAGAGGGGGGAAAAGCAGCTTCTGTAAGGGAATTCATGCTAAACCTCACAATACTAACTAAGTCAACACTCCAAGGCTAGATCAGAAGAAAACAACTCCTTTTTCTACATTTAAATATCAAAACTGAAGTCCAGGTGAGGAGTTTCAATTTTCTCTACCAACGTGCCTCCTAAAAAGAATGTTCGATATCTATGTCTGAAAAATAGTCTTTGGAAATACAGACTATAACTCAAGCAAATGAATTTAACTCAAAATATTAACATCTATACATGTCTCTGTATCTTTCCACACTCCTTGAAATACGAAGCACGGCTAAAAAGCAGAAGGATTTCCTTTGCCCCCTGAACCTGATGGAAGTTCTAGCTCAGTCCCTTCCTTCATCATAACAGGAGAATCCGGGGCTTTACTTCTTGCCCACCCCCCCACCCCCAATCACGCAGGTAGTTGAGAGATAATATATGGCTCGTGTATTTAGTTCTTGAATAGAACACTTTCTTAGTCACAAGGACTTACCAGGTGCCCCCTCCCAGGTTAAGAACTACACTGTGGATTTACGCAGCTAGCAGCAAATGACAGCAGTTCTGAATTACCTTCAGGGACTTGAATGTTTCCTTTCTCTCCCTTCTGATGAAAATTCCTTGTCTTGACTATTTATTAAAAGCCAATATACAAGAGAATGAGTCAAATTTAGCATTTGTGTCACTCCACACACGTCCCGTCATTTCTGTAACCATTTATAAAGCTTCCCTGTGTATCAGGATGATGACCTAGCTGACAAATGAAGCTTCTAACCAGACATTACTGAGATGTGATAAAGAGAAAATAGACATGATCATGAAAAATGTACAATAGCTTATAGGAAAGAATGAAAATGTCCCAGAAGTAAAAACATTAGATTGATTCACTACCACAGAATTTAATAAACATGCACACAATTTGGTGATTCTAATTATCTGTTTTCTAAAGGCATTTATCTGTTAGTTATCATGGTCTTTAAACACAACTTTTACCTGGGCTCTACATCAGTGCTCTATCTGCACAAGACATTATTCTGAAACTAATGGGCCGAAGTAAACTAATATACTACAAAGGCAAGACAATATTTTCTGTAAATTAAAACTCTCACTTGTAAAATAATGTAGCTTTAATTGATGATTTCCAATTTCCTGATTTTTCCTTGTAATTTAAAACATTCATATTTGAAGTGAAAAATTGAAGCATTCTTTCGACATTGTTTGTCTTAGACATTTGAAATGAGTTGTTTCTGCTAATGCCAGACATTACTCACATGTAAAGTAGAATCCATTTCTCAAGAAGAGCCAAAGTGGGAAATAAAGCAGGAGTAGATGTCCTCTTATGTTAAAAATTAGAATGGTGGACATACATCTGAGAAATTGATATGGATTTCAGATTCCCCTGTCTTTGAAACTACTTTCTGGGGAGTATCAAAAAGAGAATTCACATTAAAATATCAGTGAGATATAATTTAAGCTTCTACATACATCCCAATCCACAGACAGATGTAACCAACAGAGATGTGTTTAACAAAGAGAGAAAATGGGCAGCAATAAAGTGTTAAATAATTTCCCATGTTGGAAAATCAATAGCTACAAAATCCCACAGGGTTCATCTCACAGTCTCCACAAAATAAAATATCCTTTATGTAAATGAAGTTGTCACAAAACCTGGGAAAGATGAATAAATATAATTAAAAATTCATGATGTCAAAGAAAATTATACTTAATGCATACCTAAAAATTATTTTTATTGAAAAGTGACAGCTTCTTTTAACATTGAAGCCATTTCTAAAACAAAATAAATAATCCTCATAATTAAAATAATGTGCTTTTTAAATAAAATATGTAGTGTCTCACTATAGTCATTTAATAAGGTGGATAGGCTCAACTGCAGAGTCCTCATGGTTGATGTATTAAAAGCAAATTACTCAAGACTTGTGCATGAGGTATTTTTAGCTGTCTGGGAGGTAGGTCCTACAGATGAGCTACACAAGTGTTGATTGCTACAGAGGCAGAACAAAACTACACTTAGCTCAAAAACCTATAACATTCAGTTTTACTTTACATTTGTGTTCCACGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGTAGAAAAGCTACTGTCATTGTGTTATGTTTTCAAGATCCTATGATAGATTCCTCCAGCAGGCTGCCTCAGTAATACACTTGAGATTTTCATCAGTCATCAATAGGCCTCAAAAGATCTTTGAGGTTATAATAAACCTCTGTTTAATCATTAAGTAGGACTTTTGATCTTTTTCAATTTATGGCCCGGTAGCAATAAACATATCAATTTCTTAGCTACATATGACATGGAGAGGTGACATATGACAAAAGGAATCTAACTGATACTCTTTATCAGCCATTATGTGGTCTGTTCTTGTGCAAAGATCAGTTCTCTTCATTGCCTTAGAACAATCTCCAGATGACCAAATTTGCACATCTCGAGGAACTTATGACTTCCTCCAGACAATTCTCATTGAGTTCAAAAGATTTCTTTGGTTAAAAAAAAGAAGAAGAAGAAGAAGAACTGAAGGTCAGGAGAGAGTGCAGGAAATTTGGTTCATCTGTCCATCCAAAAACTTCAGGGGCTCAGAGATATCACTTCTATATCTAGTGTATCCAGTCCAGATTATGAGACTCCCAACAAGGATATGACTTTTTGGTGTTAACTATGTGTATACTCTTTACAG
Seq C2 exon
GGTTTAATGGGACCCAGAGGCCCTCCTGGTGCTGTTGGAGCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661:ENSMUST00000031668:6
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(14.5=50.0),PF0139113=Collagen=PU(15.9=61.1)
A:
NA
C2:
PF0139113=Collagen=FE(20.3=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