MmuINT1007453 @ mm10
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61887249-61890144:-
Coord C1 exon
chr10:61890079-61890144
Coord A exon
chr10:61887357-61890078
Coord C2 exon
chr10:61887249-61887356
Length
2722 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAT
5' ss Score
7.25
3' ss Seq
GCATATTTCTCCAACTTCAGGGG
3' ss Score
6.46
Exon sequences
Seq C1 exon
CTGTTGCCTCTACTCAATTCAGTGCGGCTGGCTCCACCCCCAGTCATTAAAAGGCGGACCTTTCAG
Seq A exon
GTAGATACCAATGGGGCTTCCCCATGGGCTTGGCACAATCTGGGGTCCCGACAGGCCAGCTGGGTTTTTCCATCATGCCAGAACCTGCTTCTAACAGTTACAGTAAGTTAGTAAATGTGGGCATACATAACACACAGGCCTCATCACAACATGACGCAACTATAGGCTTTCTGACACCCATTTTGCAGGCCAACTTGAAGTCTTTCAGTGGGTCATGAGTCAAGCGCCACCAGCTTTCTTGCACAGATGCAGAAATAAAGGCTCAGAAGGGTTCGGTATGTTGCCCGAGGCCACAGCCCATAAACAGAAGAGTAAGGACTTACACCCAGGTTCGCTGTCTGTTCCCACTGTGCCTCAGCTCTGTAAAATAAGAACAGGCACAGTGACTGTGATAAAATTGAGGCTCGAAGAATGATTTCCCCAAAGTTACAGGAGTAGCTAGAGCCGTGGACTTGAGAGCCAGGTCTCTGGTGTCTGCGCTCACACTCTCTGTTCAAGCGTAGACACACAGACTGCTAACTGACCACACATTAGGTGGGTGTGAGGAAGGAGGGTGTAGGTACAGCAGCTTGACCCACAACCAACAGGCCAACGCCTACTTTCCTATCTTCCTGCCTTGCTGCCTCCAAGGAGGGTTGGCCAGGAACAGGTCCCCAGGGACAACGCAGCTTTGTCTCTACCATCTGAAGTCACGTGAGGCCAGGGCCTGCCTGTCTTACTTGTTATCTGCCTTCTATGGCCCAGGTGTCCCCAGGGCCCAGGTTGCTGGGAGTGGCAGGGTCTTGAGCTACTTGCCTGGGGAGTCCCATAGCTCAGGAGCATGGATACTCATGTACCTGACTGAATAAAACCGAAAACTCACACCAACGAGCAGCTAAAAATAGAGTCACATGGTACACGTGCAGCCTATTAAGCATTCGACCCATTCCTGTGGGCTAAGGATCGCATTACCCACCAAATCCTCGAGAGCCTCTAAGGGCTCCGAGGGCTGCTCAGGAGGCTGCTAGCTGGCCAGGCCTGCTGACTGCTACTCATCCTGCTGCAGACAGACCCTGCTTTTAGGGAAGCTGAGGTGCTACTTCTAAACACGCCCTCTCCACACAGCTACTGTCTAGCCCTGCTTGCATCAGCCACTGTTTGTTGGACATTTATTGGTGAGACCTTGCTGTGAGAACTCTGCCTGATGGGTTGTAAGGGGTGGCTCAGTTGGTAAATTGCTTGTCAGACAAGCAGGAAGAGCCACGTTTGGATCCCTAGACACATGCTGGTAAATGAAGTCCTAGGATAGGGAAGACTGGGGAATCCCTGGGGAATTCTGGCCAAGCCACCTTGGCTTAACTGGTGATCTCCAGGTCCCATAGAGAGACCCTGTCTCAAAAGAAATGACAACAGCCCCTGAGGAAGGACACCCAAGACTGATGTCTGACACACACAAACATACACGTCACATACATACACACACATGTGTGCATACATACATACATATGTGCACATACATACACACAAGAACCATGCATGATCAATTGCACAAGCTGTATACCAGCTCCCTGTGGGCCATAGTTTTCATTTCCAGTTGGTAGAGGAAAACTCTATAGCAGTGGTTCTCAATGTTCCCAATGCTCCGATTACTTATTAATAAAGTTCCTCCTGTGATGGTGACCCCCCAACCATAAAATTATTTTCGTTGCTACTTCATAACTGTAATTTTGCTAAGATGAATTGTAACGTAAATGGCTGCTGTGCAGATAGTCTTAGGCGACTCCTATGAAAGGGTCATTTGATCCCAAAGGGATCCTGACCCACAGGTTGAGAACCACTGCCCTAGAGGGTCGGGACGTAGATCTGGCCACCACCTGTTGCCATGTCTGAGTCTGCCATGCCAGGATTTTCTGTACTGCCCTGATCTGGCTTCCAAAGCAGAGCCAGCAGGAGTCGACCTCATGCCTGCTACAGACTCTCTGAGGAGTAAGGGTTTCATACCACCAGCCATCACGGGACATGAGATGGCTTACCCATCTCCTAGTGATAACTCTGTATTGATTGTACACGTTATGCAAGATGGTCTCAGGTTAGCAGAAAGGGGAAGCTTGTGTAAGAGCTGACGTGCTTAGCAGATGGTGCTGGAGACCACTTCCAAAATGCAGGGAGTTGGCTGATGAGCCCTGTTCCAGTGAGCAGTAGGCCAAATGAAACTCAGTGGCCTTTGACCGAGGGTCTCATGATCCCCTGGAACAGATAATCAAAACCAGCAAACACTGAGTCAGGAAACAGGGACCCTGTGCTTCCATCCTGTCTGTAGCTGGGAGGCCTGGGGCTGAGGTGGGGGGTGGGGGATGATAGACTTGCTACATTAAGAGAGAGAGAGGCGGGGTGCAGACCACCTGGGCTGAGCTCTGGCACTGGGCTAGGCTAGGGGTGTGGCTTGTCTCTCACTCACTGACCATCTCTGCCACTGCTGCCAGGCCCCCTACCCTGGCGACCATGTCCCCTAGAAGCCCTCACAGCTCAGCCACTCAATGCCTTGGTCCTCTTCCTGCTGCCATTAGCCCCTGCATGCATTCACCGTCACTGTCACCACAGCATCGTCATCCGATCACCGCCCCACCACCCCCACCGCCTTTCCAAGCAGGTTCCACAGAGGCCTCAGCAGATGCATGGCACAGGGGGCAGTGTGACTGCTGCTCCCAGATCTTCTCTCTAATGCATATTTCTCCAACTTCAG
Seq C2 exon
GGGGAACAAAGTCAGACTGGCATCCAAGGCCCTCCAGGGCCACCGGGCCCCCCAGGACCAAGTGGCCCTCTGGGACACCCAGGACTGCCAGGGCCTATAGGGCCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806:ENSMUST00000105454:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.909 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(4.6=13.6)
A:
NA
C2:
PF0139113=Collagen=FE(53.8=100),PF0139113=Collagen=PU(19.6=30.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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
- 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