RnoINT0038982 @ rn6
Intron Retention
Gene
ENSRNOG00000000552 | Col13a1
Description
collagen type XIII alpha 1 chain [Source:RGD Symbol;Acc:1595704]
Coordinates
chr20:31474624-31477405:-
Coord C1 exon
chr20:31477361-31477405
Coord A exon
chr20:31474666-31477360
Coord C2 exon
chr20:31474624-31474665
Length
2695 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
AGCTTCCCTTTGGTTTCTAGGTG
3' ss Score
9.35
Exon sequences
Seq C1 exon
GGAGAGAAAGGAGAGGCTGGGGAGAAAGGTGACCCAGGAGCAGAG
Seq A exon
GTAGGTCAACCCGGCTCTTCTTTCTATGTGTTTGTCTAACAAGGGCATCACTAGAAATACCAATGTTTCTCCAAGTTGCTTAGCATCTGACTGGGGAAGGGTCTGAGCCCCAGAGCTGCCCTCCATCATGCAGTTTCTGCAGGATTCAGAGAACATCCTGGGGCCCCAGTAGACACAGGAAGATAAATACACCTGCCTGGCCCCGGCCACAGACTTTGTCATGAACTTTCAGAGGAATGCTTTCTAGAGAGGCAGGGTTCCTTAGGAGACGTCTCAGAAGGGGAGAAGAAGATTGAGGAACAGGCAGTTGCTATGGACATGGGCTGTGCAGAAAAATGGGTCGTGTTGTGTACATTTGCACAGAGGAAGCAACAGAGATCTTGGAGATGGGAGGGAGAAGATGTTTGGCAAGAAGGCCTGAGCAGTCCAGTAGCCACCCGACAGCAAAGCAAGAGACCACCAAGCTTCATAGTCCCCCACGAGCTCTCCTGGCCCGTCACCCTTTAATGTCACTGGCCCCGTCTGAATCAAGCAAAACGGACCTAATTGTACGCTACCACTGTTCCTTATTAAGAATGGGTTGCACCCTGAAGAACTGATCCTAGATTCTGGAAAAGCATTATACACACAAATGTCCCCCCCCCAGAAGTATTTCAAGTCAAAATTGAAAACAGACAGTGTCCCTAAAAAGAAGGAAGGGATAAAAGTCCTTAGGCTAATAAGCTCTTAGTAATAGCTTTGTCCATGGCTGAGGGCCTTTCTCATGCCAAGAGTGGCTTCCAGCCCAATCCAAGCAGACGGCTGCTCTCCAGCACAGCGGCCAGTGTTTCCTCGAGGAAGATGGCTCATAGAAGAACAAACCCAAAAATAGAAAAATCAGTTTTGCATCAACTAGAAAAGACTAGAAAATCAAGTTGTATTTACGCATCCTTGGAAGTACGTTAATGTATTCAGCAGTAGCTGAGATGTTCCAAAAGCTAGGGAGGAAGCCAGGCAAAAAATACAAGCAGTCCTCTCCATTAAATATAACAAATATATTGGTTTTCCTCCTTTAATTCTCTTTCACTTATAAACCATTTAATAAGTGTGTGTTGCTCTTAAACATTTAAAAGTTGCCATGCAGGTAAAATGGATTACGGGAGAGTACATAGGTGTCTAAAACATATTAAACAAGAGTAGTTCTCATAAGCTAGACATGGCACACGCTGGGGGATCTCTGTTATTTTGAGGCCAGCCTGGTCTACAAAGCCAGTTTCAGGACAGGCAGGGCTGTTACACAGAGAAACCCTGTCTCAAAAAAAAAAAAAAAAAAGAAAAGAAAAGAAAAGAAAAGACAACAACAACAAACAAAAGTACTTATGTTGTTTTTGTTTTTGTTTTGTTTCGAGGCACAGTCTCACTAAGTGGCTCAGGCTGGCCTTGAACTCACAGAGATCCACTGCCTCCTGAGGGCATCACCACGCTTGGTGGCGTGTGGATTTCTATATGCACTATTACGATCAGATCTATACATTATTTATAATAAAAAGTGTGCAGTGTGCATGCATGCCTGCCTCTGTGCGCGCGTGCATGTGTGTGTGTTTATGTGTATGTGTGTGCATGCGTGCATGCATGCGTGTGTTGCTGGAGATAAGATCTAGAGCTTTTATGCATGCTAGCCCAGTGCTCTACCACTAAGCTACAGCCCCAGTCCAAGTACTCTAGTACTCTAGTTTTATTTCTGTTGCTGTGACCAATTAAAAAAAAAAAAAGAGGGTTCCATTTAGCTCCCAATTCCAGGCTCTTTGTCCATTGATGCAGGGAAGTCAGGGTCAAGGAAACTGGAATCAGCTAGTCACGTCACATCCACAGTCAAGAACAGAGAGCAATGAATGCTTGCAAGCTCGCTCACTTAGCTTCATTTCTCCACCCAGGCAGTTCAGGTATTGTACCCAGCTTAGGGGATGGTGCTGCCCACAGTGAGCTGGCTCTTCCCACATCAATTAACCTATTAACCTATCACAGGCCAACCCAAGGGAATAATCCCTCACTGAGAACAAAGGCTGTGTTCTCTCCAAGATCACATGAGCAGAACCACCACAGTCTGAGGGACATTGGTGTTTTCTTATCCTGCCTAAATCCCTCTTGCTGCACCTGCCCTTGAAGGAAATACAACCATCACTGGCCTATCCGTTACAAACCTGGGGCCGAGCTAGTCTTGAAGAATATTCTTCAAGGACTTCTCAGCCTCCTCTGGCTTCAGATAACCAGTCTCAGCTCCCTTAGGCCAAGAATCTCAAACTCCCATGTCTACCAGATCCAGGCCACAGATGAATGCCAAGAGGCCAGAGTTGATGACAGCAGGGGGTGGAGTCCGGGCAGACTGGAGATCATGGCTTACTTGATGAGCGGGGCTCTTACTCCTTTCCTGGGCAGTCTGGGCAGTGCTTGCCATAGGTAGCATGGCACAAATCCAGTGCTAGCTAAATGGTGTCCCATGGTGGCCTGGCCTGGAGGAGTAGGTGTTCTGAAAACGTTTCCTGAAAATGTTTCTGGATTGACACTGTGGGAGACCAACAGTTTGCCCTGAGTCCCTGTGCTAAGTCTCTTTTAGGGTGTGTACTGGCCTGATCTTCAGTGGCAATCCTGTCATCCCGTGGCCTTAGCTGGACCAGGACCATAACAGAGCATAACACAGCTTCCCTTTGGTTTCTAG
Seq C2 exon
GTGCCTGGGCCGCCAGGGCCAGAGGGTCCTCCAGGACCGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000552:ENSRNOT00000046537:27
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=FE(17.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(16.5=100),PF0139113=Collagen=PU(17.5=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
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]