MmuINT0039038 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61306316-61311959:-
Coord C1 exon
chr10:61311924-61311959
Coord A exon
chr10:61306403-61311923
Coord C2 exon
chr10:61306316-61306402
Length
5521 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
GACTAAACCATTGCTCACAGGGG
3' ss Score
3.64
Exon sequences
Seq C1 exon
GGTTTACATGGACCACCCGGGGACAAAGGAAACCGG
Seq A exon
GTAAGTCTGAGCCCTCGTGCTCTGCATCTGGTTACTAACGTCTTCATGATGGGATGGAATGATCAATTGGAGGCTCCTGACCTAACAGGACAAATGTTCTTTCCCTATAAATCATCCTAAATTGAAAGGCTTTCTAACGAGGGGCTCCATGCCATACACGCAGGGAACCTGAGGCCCAGTACTACAGTTGAAGCCAGTATTTCTCATTTCCAGAGAAGGCTCAGTGAATCTCACAGCAGCCATCAGATTAGCATGGCCATCTAGTAACAGGAGCCTCTCATCCAGCTCTCTCTACGTTGCCCTGATAACCGGCCCCTTAGTGATATTTTTAGATCCATCGTCACCTCATCTTTGCCTCCTGAAACTGAGATTTGTCAGGCATTCCAGGCCACTATTGGTGACTGAGAAAATAAATTCCAGCTCTGAGAACAGCCAGCCAAGCCCTAAAAAAAAAAAAAAAAAAGAGTATATCCCAGCTGCTGTTCCTCTTGGAGACTTGGCAGGGAATGGAACGGACTGCATTCTCCAAATCCTCCCTCCTCCCCTTGGCTCCTGCGGTCCTCAGAAGGATTTGTTAAGTGTCCCCAACACCATAGGCGTATAATGGTCATGGCCTTGGGCATTTGGGTCCAGCAGCAATAATCTAACTACATCTGGCCAAGAGACAGCATCTTCTCCATCACCTCCTCCAGGGCCCATCTGTGTGCAATGCACACACCCTAGACCGTGGTTCTCAACCTTCGGGCCAAGACCATTTGGAGGTCAGATGACCCTTTCAGAGGGGTCACCTAGAACCAACAGAAAACACAAATACTCACATTATGATTCATACAGTAGCAAAGAAAGTAGCAACGAAAATAATTTTTTGGTTGGGGGGGGTCACCACAACATGATAACCGTATTAAAGGACCGTAGCATTAGGAAGGTTGAGCACTGCTGCCTTAGAGGACCAAGAACATCCTCCAGCAGGCAGTGAAGTTCAAGGACCTTACATGGCAAGGAACGGAAGGAACAGGCAAAGGGCCACTGTCCAAAACAATGGGATATGGTGAATTGAGTTTCCCGGTGAGACAGAGGCAGAGCACGTGGATTTCGGAACCTGGGTGATCTTTGACATTGGTCAGAACATGTTCCAGGAACAGAATCTATCAGAATCTGTATGTTTCTATCTGGCCCCAATTAAATCCATCATCCTTGATGGATTAGCTCAGCACTTCTAACCCCCTAAAGCCTCCTCTCCAGCAGCCACACAAAAGCAAGTCAGCCTGTCCCCTAAAACCTACGAACAAGTGAGAGGAGGCAGGGCCACCCCTACCAAACCGTCAATGGCGAGGCTTCATGGAGTCCACGGCAATGACCTAATCCACTTTCAGCTGTGTGGCTGGTCTCTGAGTCTACCAACCTGATCATTCCATTTCCTCGTTGGTTTACAGACCTTCTTAACTCCTAACTTCTAAAACTTCCTAATGTGTTCTGGTTCTCTTTATTACGCTCGGTTCACATTTTTTTCAAACCTGTTTCTTAAGACTTTCTCTGCTGGCTGGAGGCACTGGAGCAGTTGAAATGAAGACAATGCTTCTGCCGTAGAGAGGAGGCTGGGTTGGTCAGTGAGGGGCCCTTGTCACAGAGGATGAAAAAAATGGACCAGGCTGCTGTCTCTGATGCTAGGCATTGTGGGAAAATCTTTCTCCTGCACTTCCCCTTCCTGCTCTTTGATAGTTTCTCCGAATCCTAGATAGAATGTCTCTTCTTTGGAGTCAAATTCAAGGACTGAGGGTATAGCTCAACTGGGGGAATTGTTTGCTTTGAGCCCTAGGTTCCAGTTTAATACTTCACAAAGCTCAGTGGGTACCACACGCCTGCAATGGCAGCACACAAGGGTGGTGGGGGAGTACAAGGCAGGAGGATCGGGGAGTCACGCTCATCTCTGGCTACATTTCTGGCTCAGAAATCCAAGAAACTGAAGGTCAAGCTCAGAAAGGCAGTGAGGCGCCGCACAGAGGGCCAGATGAATTGTCCCAAATGGCAGGCTTCAAATCAGGGAGCAACGAATTTTTCTCACCCAAGAGAGTCAGTTCTCAGGATGCCAGATGGAGAGGAAAAAGACACTGGGAACCTCAGCCACCTCATCCAGGCCTCTGAGCCACCAGCCCTAACGGGGCCTAGAGGGAGGTGTATGATAGATACACTTTGATCCAGGTGACATGTCAGAGGCCGAGGCAAGGTTCGGAGTGTCACCTGGGAAGTGACGCTGGAGATATCCGGTGCTCCTCCCTGTTCACCACAGGCAGCCCTCACAATTTGCCCTCATTGAGCTTTGCCTTATCCTGCCTGGGGAATCCATTAGGAACCGGTTCCATCTCACGTGATCCAAGACACAGCCTTATGATTTTACTGTTGGGCGGGCAACATGGCCTCAAAGGCAGAGGTGCCTGCCACCAAGCCCGACAGTCTGAGTTCAATTCCCATGTGGGAGAAGGAGAGAACTGACTCCCATTAGTTACACACACACACACACACACACACACACACACACACACACACAATTATACTATTGCATGTCATACCCAAAACTGGTCCTACACCTCTTTCCTGTTCACGGAATAAGGAAAGACCATGTTACCCGATGGACAAGGACAGAATCCCAAACAGGAAGCCTGCTAAGGATACACAAGACCATCAAAGGGGTGGGGGGTGCTCTGCTCTCATCTCTAAGGGTACCTTTCTCCTACACATGCCCTACCTTGTCTCTAAGTGACTCAGCGAACTTGGGCCAGGAGTCCTATTTACAACAAAAACACTGGTCAGTGCCACACATGGCCCCTCAGGCCTGGGAGGTAGAGGCAGAAGGGTCAGGTGTACACAGTCCCCCAACTACATATCAAGTGAGAGGCTAGTCTTGGTTATAGGAGAAGACTCAGTTGAAACAGCAATGAAATGGGGTCAAAGTGTAAGGTGCCATCACTCTGGCAAGGTAATTACCAGGACATGGTTTGATTGGTTGTTACCACAGAACTGCCTGCAAGCCAGCCAGTGGAAAAAGTCCCAGCATGCTGAGCTGCTTCCACCTCTGCTGGGGATGGGGATGGGGGAGTGTGTCGGGGTGCATGCATGTCTTGCTCCCTGGGTCCTTCTGCCCCTCCTTTCTCTCCCTCTCCAGCCTCTATAGCCTCAGTCTATCTCTTATTTCCTCTTCCTTTCCCTCAACATATGCACCCACTAAACTCCCACAGCCCCCATCCCTCCCCCGCCTTCTGGCTTATGTCAGTCCTTCACACTCATCAGGAATGTGGGTCACTGTCTGCCCCTCCCCTCTTACCAGCTGGAGCTGGGGGTGGGGGCATCTCTCGTATGTTCCACTCTGGGGTAGGCAGGAGGGGACATGTAGGTAAAGCTGTAAGTCCAGAATCTTCCAGAACACACGATGTGGGGGTGATGCCTTATAGTGTGAGCAGCCTACACTCTGACCTTCAGGCAAATCTTCTAAGGCCTGGAACCACCCCTTCAGCAGCCCCACCCATATTCTTCATTGGGAAACTACTCATGACTCAGAAGATAAGGGCCTCACGCCCAAGGACACCTACCTCTAAGGGCAAGGACCCGGGTCTTCCCATTCCAAAGAGCTGGTGCCCCAGCTTGTCCACACTAAGGGGATCCTCATGCCCAGGTGGTTTCATTGGTGTGTGTGCCTTTGATCCAAGGACTTCACTGCCTGGGCACACACTCATTAACACTCATCACTCTGAAAAGCCATTATGTGGACAATATGTGGACAAACTACAAACATCACTGGAATTTAAAAACAAACAAACAAACAAACATACCTGGGTTCATGTTCAAAGATCTGGGGAAACATCAGTACTACAGCAACTTACAAATGCAGGAACACCACAGACAGGACAAGACCCTCCTGGGGAGCATCCGTTCCCATACTAGGTAGCAGGAGGCGTCATCACCACAATGGGCTGAAATCACCTTCCATTACTGAGAAATACGCCGGTAATCATCTCTTATACACAAGGTCGTGCAATAATTTTGGGAGCAAGTGTAACACACCCATTTTACAGGAAGAAACTGGACACACACATGAAGAAACTGGAGTTCCGAGGGGTTCAAAGTTAGTAACTGGCAGAACTCACCAAACCTTTGGCCTCCCCATGATGGAGCAGTCATGTACAAATCCTGAGGCATGGGACAATCCATTTCCACAGAGGGAAATGTCTGGGGACAGCCCGAGGGACACTCATGGCCCATTTTTAAAGAACCGAGACATATGAAAATTTAACTGCAAATCCATTTCCAGATGATGTCATTTCCAGAGGCCCCAGAGCCCTTCTGTAGATGAACCCCAACACATAATAGACGGGGTTCACTTAGGAGCAGGATTTTCAGAAACAAATGAACTCCCTGAGCTGGCTGGAACAGAGTGTGCCAAGATGCACTTACGGAGGTCAGAAGACAACCTGGAAATCACTTCTCTCCTCCTGCCACTTGAGGATTCGCCTCTAGTGGTCAGGCAAGGTAGTGAGAGCACCTTCTTTACCTGCTATTAACCACATCACGGCCCAGCAGGACAGCTTCAAATAGTGATGGTCTGAGACAATAATAAATCAGAGCCAGGGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACCGACTGTTCTTCCGAAGGTCGTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCTGTAAGGAGATCTGACCCCCTCTTCTGGGGTGTCTGAAGACAGCTACAGTGTACTTACATATTGTTAATAAATAAATCTTTAAAAAATTTTAAAAATAAATCAGAGACAGACACAGCATATGGAGGATCAGCCTGAGACTCTACACATGTGCACACACATGCACCATCCTGCTCACACATGTGCAGACTGTAGTCATGTATGCACGTGCCTATAGCGGGGCTCTGACTACAGTCACCTTGTCTCCTGAGGTACTGGCATGGGCATGAGAACTAACTGGGACAAGAAGGGGGCTAGAAAGTGGGCTCAGTGGCTAAGAATGTGTCCTGCGCCTCCATGGGACCCAAGTTTGGCTCCCAGCATCCACATGGGCCAGACTACAACCACTGTGACTCCAGTTCCAGGAGCCTCTGACACCCCTGGCCTCCACAGACACTGGCATTCGTGTGTATACACACACACACGTACACCATCCTTTGCTAGGTTTAAGAACAGCAAAATTGGGCACCACAGTCCTAGGTGGCCTCTTCCACTTCGGCTCAGAGATGCCCCTGCTCCCGCCTCCCTCTCCTCTCTCTCCTTTACCCTTCTCCTTTGCCAAAACCCTAGGTACTCATGCCCACTCAGGTGGGTGTGTCCCATAATCCCACGGGAATGCTGACTTAATTAAGAAAGTCTTTTTTTCACTCCGCCCTTTTATGTATCATTTTCTCTCTCTAATGTTAACATGTGAACGATCCTAAAGTTTTGATGATGTGTTGTTGTTTTTCCCCCCTTCTTACCTTGGACTAAACCATTGCTCACAG
Seq C2 exon
GGGGAGAGGGGGAAGAAGGGCTCTAGAGGGCCTAAAGGGGACAAGGGGGACCAAGGAGCACCTGGACTAGACGCCCCCTGCCCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:38
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.967 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(12.5=83.3),PF0139113=Collagen=FE(15.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(41.4=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: