MmuINT1007498 @ mm10
Intron Retention
Gene
ENSMUSG00000048126 | Col6a3
Description
collagen, type VI, alpha 3 [Source:MGI Symbol;Acc:MGI:88461]
Coordinates
chr1:90811259-90816535:-
Coord C1 exon
chr1:90815951-90816535
Coord A exon
chr1:90811832-90815950
Coord C2 exon
chr1:90811259-90811831
Length
4119 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
TCCATCTGTTTTCCTCGTAGAGA
3' ss Score
9.72
Exon sequences
Seq C1 exon
TCATGGAAGTCAACAAGAGGGACATAGTCTTCCTGGTGGATGGTTCCTCCAGCCTGGGGCCATCCAACTTCAATGCCATCCGAGACTTCGTTACCAGAGTCATCCAGAGGTTGGAAATTGGACAGGACCTGGTTCAGGTATCAGTGGCTCAGTATGCAGACACTGTCAAGCCTGAGTTCTATTTAAATTCCTATACCAACAAAAGGGATGCCATAACTGCTGTACGGAAGATGAGGGCCCTGAATGGCTCAGCCCTGTACACGGGATCTTCTCTGGACTTTGTTCGAAACAACCTCTTCACTAGCTCAGCCGGCCATAGGGCCGCTGAGGGGGTTCCTAAGCTCCTGGTGCTGATCACAGGCGGTAAGTCCCTCGATGAAGTCAGCCAGCCTGCCCAGGAGCTGAAGAGAGGCAGCATCATGGCCTTGGCCGTTGGCAGCAAGGCCGCCGATGAGGATGAGCTGAAAGAGATCGCTTTCGACTCCTCCCTGGTCTTCATTCCCGCTGAGTTCCGCCCTGCTCCCTTGCAAAACATGCTGCCCAGCCTGATGGCACCTCTCAGGACTCTCACTGGAACCACGGAAG
Seq A exon
GTATGGCGGCTGTGGATTACACAGGCAGGAGGGGGCTGGTAGGCAGAAACTTTGAGAAATACCCGCTGGAATACTGTTTAGCCGACAGACTGCTGTTTTGTGTTGAGAACAACCATTTAGTTCTCCTGCAGGGTTGAAACAGTAGAGTTGAAAATGTCCCTCTGCACATGCATGTGATTTTAAACTGTAGCATCACAGGGTCACCTGCCTGTACAGCTTTTGGCCACAGAAGTCACTCTCAGTTCTTTGATGGACATCCCTTCTATTTTTATTAGTGACTCTTTCCAGGAACCTCCCCTCAGCCCAGGACTTTCCTTTCCCAAGCTGACAGGATCTCTACTCACAGATGATGTAGTACCCTCAGCTCTTAGCCCCTGTTTTCGCCCTGTATAAGGGAGCCTCTTAAACAGGAAAACATGCTGATAGATGGGTGTGAAGACCCAGCCCGTGGTCCTTCAGCTCCCTCACTTAATATGATGGACAGTGCAGAGTTATTTCTAGAGACACTGAAGCGCTCAGTCTGTGAACTGGGTAAATGCAAACCTTCATCCTCAGTGAAGAGAAGATGAATATCCTGGAATCCAGCTTTCCCCTCTCACAGACCATCACACAGAAGGGCTGTACAGTGCATGAACCTACTGCATGGGTGCCTGCTTGCTCCTCAGACCATCTGTTCTTGAGAGCCCTCAAATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCACTCTTTTATAGCCAAAGTTAAATGCATGAACATAGGATCCAGTTAGTCTGAATTACAATGGGGCATGGGAGGGTAGTAAGTCTATGTATCCTTCAGTGTCCATAGGAGATAGGCCAATTCCCTCCATCTGTGAATACAGAAATCCACAGATGCTCAAGTCCCTTCTTTAAGATGGTACAAGTGCCCAAATGTAATTTGTATATATCCTCCTATATATACTGTAGCAAATGCAAGGCTAGCATTGTAGCCAATTATATAGGAAGTACTGAGAAGGGACAAATATGATTTTTTTCCCAAATATTTTGAGCAATGGTTGAATCCCTAGATATGGGACCCACAGATAAGCTTTTCTTCATGGCCAAACACAGGATACAATCTCTTCGTCACCCAACTTCTCTGCGACAAGACACATGACAAAATCAAACTAGTGGAGGAAGGCTGGTTCTGGCTCACAGCCTGAGGATGCTGTCTGCAGTGGTGGGGGAGTCCTGGGAGCAGGAGCTTGAGGTAGCTGGTCATATTTGTAGTCACAAAGCAGAGAGAGACAGATGCTGGCACCCAGCTGGGACGTTCTCCTTCTTCCTCTCGCCCAGGAAGGACCCCAGCTCACAGAAAGATGGCATCTCCATTTAGGGTGGATCTTCCCACCTCAATAGCTCAATCTAGAAACTCCCTTATAGAATACACGGAGGCCTGTCTCTTAGGTGATTTTAGATTCTGTCTAAGTTGACATCTATTTTAACTATCTATGGTGCTACCAAACCCATGGTGCTGCCACATCTCCTTGGAGGCTTTCTCCTGGGTACCCTATTACTTGGTACTGAAATGACCCCTAATCAGAAAGGAGGATAGGGGGATGAAGACTCCAGTTGTAGGACCACATCCTTTGATTGGCAGACATCCTTTGATTTAATCTTTGATTAGAGAAGCTGTGTTCCAAGGTCCATGTGGGCTGATGTTTCTTGAGTTTTGGGGTAGAAAGATCCCTCTATGTGCACCCAGGTGAGTCCCAGAGGGTCCAGCCAGCATAGGCGAGCATCCTGTGACTGGATCTCTGGAGACAATGAGCAACAGAAGGGCCAGCACCCTGTGGACTTCAGTTCCAGGGAGGAAACACTGTTTTAGGACTCTTCTAGTGATGTTGGTTGTAAACATTCTAACTCTAGCACTTTGTCTGTCTGTGAGCCATCTCGGTTTTGTACACTTGGCTATCAGTGTGCCTCACAAACTCCAGCCACTGCAAGGGGAAAATATGCAGCCGCTTGCCATATTTTACCAGATGACCCGCTCTGCCACGTTGACTACCTCTGTGTTCTGAGTGTGCCATGTGTGCCCATGAGGGCACACATGGGAAGCCCTCTCAGGGGCATGTCTCACTGTGTTTTCTGTGCTTCACTGCAGTTCACGTAAACAAACGGGATATCATCTTCCTTTTGGATGGCTCCGACAACGTTGGGAAAAACAATTTCCCTTATGTGCGTGACTTTGTAACCAACCTAGTTAACAGCCTCGATGTTGGAAGTGACAATATCCGTGTTGGCTTGGTGCAGTTTAGTGACACTCCGGTCACGGAGTTCTCTCTAGACACTTACCAGACCAAGTCCGAGCTGCTCGCTCACCTGAGGCGCTTGCAGCTCAAGGGGGGCTCCGGCTTGAACGCAGGCTCTGCCTTGAGCTATATCCATGCCAATCACTTCACGGAGGCAGGAGGCAGCAGGACTCGTGAACACGTGCCTCAGCTGCTGCTCCTGCTCATGGCCGGGCCCTCTGAGGATGCCTATTTGCAAGCTGCCAATGCCCTGGTGCGCTCAGGCGTGCTGACCTTCTGTGTGGGGACCAATCGGGCGGATAAGGCTGAGTTAGAGCATATTGCTTTTAATCCCAGCCTGGTATACCTCATGGACGATTTCCGCTCCCTGCCATCTTTGCCTCAACAGCTGATTCAGCCCCTAACCACATATGTTAGTGGAGGTGTACAGGAAGTTCCACTATCCCAGCCAGGTAAACCTCCCAGCAGTGTGGGCCCCTTTCCTTCTCCAGATGCCTCTCTGGCAGCAGTAGCCAAAGGCACCTCAGAGCCTGTGACTTGTGGAAGAATGGTGGGTTCATTTGGGCTGGGACTGGTTAAAGACAGTGTGTTGGCAAATGTAGACCCTAAGTGTAGAACATTCAGCTATGCCCTGTTCATGATGATGTCTCACATTTACTGAGAAGATGAACAAGGTGGACATTCTAGAGTTCATAAGGGAGAGGGGGCAGGGGAAGGGAAGGGAAGGGGAAAAAGAAGGAAGGAGACAGAAAAATTGATGATGATTTGTTACATGACTATGTATTGGCATCCTTTAAAGCTCGAAATCTTCCTTTATTCAGACTCGGCCATGTTTAAAAAGCACCTGAATACAACAAAGAGTCTGTGTCGCTACTTCTGTGGCAGGTGGTTACTATTATGTCCCTTAGTGGTGGATACACAAGACCTACCAGTCAGATGGGTAGCAAGCCTGAGCCAATGGCTATCTCACCGAAGTAGTTCTCAGAACTGTTTGAGATATTTACATGATGGTGTGCCCCCTGCCCCCTTGCTGTCACCTGTGTTTTCTACAGTCCAGTTTTGGTAAATTGGAAATGTTTGTAGAGGTTTTAACTTTCCACCTCCCAAAGCACCGGCAGGTATTATTTTGAGTCTTAACTCTTGACCTTACAGGTTCAGAGGTTCAGTCTATTATCATCAAGACAGGAGAATGGCAGCGCCCAGACAGGCATGGTGCAGGAGGAGCAGAGAGTTCAACATCTTGTTCCAAATGCAAACAGACAACTGGCTTCTAAGCAGCTAGGATGAGGGTCTTAAAGCTCATGCCCACAGTGACACACTTCCTCCAACAAGGCCACACCTACATCAACAAGAACACACTTCCAAATAGTGCCACTCCCTGGGCTAAGCATATTCTAACCACCACACACATCAACCCAGATGTCAGTGGGAAGTTAGTCTGTAACTGGTCTCTGTCACATGAGATAGAAGACAGTCTTTAGGGAGAAGTATAGAAAGGAATGGTTTTGATGATTTTATTTATAACAACAAGAAAACGTTGTCTATTCTCAGTGGTTTAACCTGCTGCAAGAACAGGGTGGGCAGGCTTTCTGGCTACTTGCTTTGTCAAGAATGTCTGGTGGCAGGCTGTTAGAATGACCAGGCCAATCCCATTCCTTTGCAAATTTGTGCTGCTCTGGAACAGCAGAGGCCATTGGCAGGGCTTTGTTCCCCTCCCTTGCTGGTACGGTGATGTCATAAGAATCAGGCGAACTCTCACATCGTGGCAGTACGAGGCAGAATGTACTTGATGTCAGGGTCTCTTCGCTTACTGTGTCCATCTGTTTTCCTCGTAG
Seq C2 exon
AGAGCAAGCGGGACATTCTTTTCCTCTTTGACGGCTCAGTCAATGTCTTGGGTCAGTTCCCTGCTGTCAGAGACTTTCTCTACAGGATCATTGAGGAACTTGATGTGAAGCCGGATGGGACCCGGGTAGCAATAGCTCAGTTCAGTGATGACGTCAGGCTGGAGTCCCGCTTCAGTGAGCACCAGACGAAAGCTGAAATCCTTAATCTCGTGAAGAAGATGAAGCTAAAAACAGGCAAAGCCCTCAACCTGGGCTACGCCCTGGACTACGCGCTTAGGAACATCTTTGTGAGGTCGGCTGGCAGCCGCATCGAGGATAACGTGCAGCAGTTCCTGGTGCTGCTGGTTGCTGGAAGGTCGTCAGATGCTGTGGCCGGGCCTGCAAGCTCCCTGAAGCAGAGAGGAGTGGTACCTTTCATCTTTCAAGCCAAGAACGCCAACCCCAGTGAGCTGGAGCAGATTGTGCTGTCGCCTGCATTCATCCTGGCTGCAGAGTCACTCCCTAAGATCGGAGACCTCCAATCACAGATTGTGAGCCTTCTGAAAGCAGAACAGGGTTCAGGCCCTGTATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000048126:ENSMUST00000097653:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=87.8)
A:
NA
C2:
PF0009223=VWA=WD(100=90.1)
Main Inclusion Isoform:
NA
Associated events
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
- 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