MmuINT0039013 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61349997-61352892:-
Coord C1 exon
chr10:61352827-61352892
Coord A exon
chr10:61350105-61352826
Coord C2 exon
chr10:61349997-61350104
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-Col13a1:NM_007731:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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(56.5=100),PF0139113=Collagen=PU(20.0=30.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]
Other AS DBs: