RnoINT0038990 @ rn6
Intron Retention
Gene
ENSRNOG00000000552 | Col13a1
Description
collagen type XIII alpha 1 chain [Source:RGD Symbol;Acc:1595704]
Coordinates
chr20:31458322-31461782:-
Coord C1 exon
chr20:31461696-31461782
Coord A exon
chr20:31458361-31461695
Coord C2 exon
chr20:31458322-31458360
Length
3335 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
CATTCTCTGCCTCCTTGCAGGGA
3' ss Score
11.77
Exon sequences
Seq C1 exon
GGGGAGAGGGGGAAGAAGGGCTCTAGAGGGCCTAAAGGGGACAAGGGGGACCAAGGAGCACCTGGACTAGACGCCCCCTGCCCACTG
Seq A exon
GTATGTCTTCTGTTTCTCCCTCGAATTGTTCTGAGTTTTTTCCACAGGGTTGCAGGTTGGAAACAGAAGAAGCCAAAAGCATTGAGGAGCTGAGCTCCACAGATGCCACCAAGCCTGTCTGTGCCTTGGCAGTCCTGCCTGCAGAGGGTGGGCCTCAGAGCCACAGCTGCAAGCCATTCTGCTAAATCCCTGGTCTTTGAGTCCCCATCCTTTGAAGATTCAGAACAATGGATGGGTGGAAAGGAAGGGAACCCGCAGGGTTTGGGTAGAAGGTCTCAGGCTCTGTCCCCAGCGTGCTTTGCAAACCCACCATAGTGTTTATGGCATGCAGATTTGCAACCTTTGTGGCATGGCCACCTCTTTTGGCCTGCAGCTCTCAATGTCCTCACTTAGGTCAGGATGCAAGACCCCAGGTTAGTCTCCTGAGTTCTATACTGTGTAGAATAAGGTTAGACAGGGGGCTTTTCGTGTACTGCCCAGCTAAGCATGGACTACTATATCCATGCTCTTATGCCCAGTCAACCAGCTAAGACCCAGGGAGCTGCAGACCAAAGATCAGCAGATAGCCCCAAGCAGCCTCCCAACAAGCCAGCAACTGATGATCGTGGCGCATCAGCCTGGCTTCTCCAGAGACCTCTCAAAGCACTAGAAGCTCTGAAAGGAGAGCGGGCCGCTGTCAAGCTGCGGTTGTCTGTGGTTGCGCCTGGAAGGGATTGCAGTGCAGGAGAAGCTGGCTGTGTGTCATCGATGCACCTTCCCTTTCGTGTGTCATAGCCTCGGGGTCTGCGTCCTGGCCAGGGTAGGACTGGACCTGTCCCACTCCGCAGCTGGAGGTGGCTGACTCTGACCTCAGTAATCACCGTGGTTGGTTTTATGAACAGGGCCACCGAGGTTTTAAAGGAGAGAAAGGGGAACCGGGGCTGCCAGGGCTGGACGGACTGGATGCCCCATGCCCTCTGGTATGGCATTTTCCTCCTTGTGTGGCCAGTTTGGGCTACCCCACGTGTGTGGTGTGTACCTGTGTGCCTCCTGCTTCCCTTGTTCTGCTCTCCGGGCTCCTCCTTACTGCTGCTTCCTGGCCAGGAGTCACCCTGCCTAGAGCATTAGTGGCTCCCAGCCGTGTTGTGCTTTGCATGCGATGTGCCCAATAGCATTCTCTTGGCATCCTCCTGCAACTGCTTCTGAAGCACCACCCCATCATCCTGCCCACCCCAAAGCCAATCCTGGCTGCATTTCGTCCTCATTGCCTGAGGATTGCTTCTAGACCCCTCTGGAAGCTAGGGGAGTGAAGGAGTTGGGCAGGTTTTTAGAACCGTTTAGGTTTTTGTCTCCACACGGTGCACTTAGCCTCGAATACGCACACAAAACAAAACACAGAAGTGAGCTGACGGTCACCCTTCCTCCCCTGCCCAGACTCCCCCACGGTTTGGCAGGGGACATGGGGTGCGCTTCTGGACAGAGAAGTTCTATAAGGTAGCAGTAGAGGCCGCCCTGTCTATTCTTCCTGACTAGATCCCCGCATCATGGCCCAGGCGTCACCATCAGAACTGGATTATAGTATCAGATGCTAAAGGCCCAGAAGGCCCTGTTTAGTGTCTTGTCCTTCATCTTAAGATAGCTTACTCTGAAGAGAGAAGTGGAAAGGCCTCCCGTGTAGTTAGGAAGAGGCAGTGGTGGCCAAGTACCCCTGAGATGTCTGGAGCTGAAACTCAGGAGCTGGTTTCCCCCACACCTGGTCTTGCTCTGGATGGTGACTGACTTCCTAAGTATCTACAGGATCCTCTCAGCTAACTGTACAAGAGACAAAAGGCAATGCTGACCCTGCAGGCACGGGTCTAGCCGTTCCTCCTTGCTTTCCATTTCCCCAGGGGATCCGGAGGCAGCTGTCACCACCCAGTTTCCCAGCCTCAAATCTCCACCCTGTCATTCTGGAATTCTCTTTGGATGATACAGTCCCTTGAAAGGATGTCTTAGGCCACAAGCACAACAGAGCCAGCACAGGTCACGCGCTCCGGGTAGCAAGCCTGCTGACACTGTGGCCTGCCCTCTCACTCCTAGTGTGCAGCATGCATGGTGGATGCCTTTCTCCATATGACTCCAAAGCACTTCCACTCATTAAAACTGGGTCTTTCCAGGACCTTAGTTGTGCCCTGCCCCCACCCCAACTTTCACTCCTCCACACCCCTGCCGTCTGTGCACTCTCAGCTCTGCAAAGGCACCTAGCCTTTCTCTGCCCTCTGCCTACTTTTCCGCTGCACTGTGCCACCATCCATGTCCCGAGGGAAATGCCCTCAAAGCCCCCTCTCCTCAGAGTTAGTGTGAAGTGTGCTATACCGCGGCAATGGGATGACTTGGCATGGCCTGGTGGACTGTGAAGGAGACAGAAGGTCACCATGAAACTGAAATGCATGCCCCCTACAGGAAGTCCTTCCCGAGCCCAGAGGGAATATATATCATTTGACTCTTCAAAATGATATCTTTTCCAATAATGATGTGTTCTTTGTCTTGGACTGGCGGAAGTGGGGTGCAGGAGCTACTGACAAAACTTTAACGCATGCTAGGTTTGGGCTGGGGCAATACCTGTGGCATGCTGGGTGATTGGGAGGTCCTGCTGGGTGGGGGAGGAAACCCTAGAGACTGTAATTATAGGATGGGACTGATACCTAGACCTCTACTTCTGGTCCAGCTTGGCCCTCCCCTCCAGCCTGGCCTCTGATGTGCTAGAGAGACCAGAATGTCAGGCCTAAGAAGCCTTGTGAAAGTTCCCTTACACAGGCAGTACCCCAAGGCTGCTGCTGCCTTGCCTCAGAAAGCACACAGTTGCTTCCCATCCTGACACTCCATTTCCCCCTGGAAAATCTCCCTGTGGCTGTCTGTCCCTTACTACCCCATTCCCACCCATTATTGGCCATTATCTGGGGCTGTTTGGATGACACCTCCCATTGCTCAGGAAGAGAAACAAGCTCAAGCAGGCTGCGGAGCATGGAGAAACTGTCCCATCCCCCTTGCAGAGGAAGGCCAGGAGGCCCATGTGCTGAGTTCTTAGCGCTCCACTGAGTCAGAGCCGTGGGCATCTGTGCTGGCCAACCCCACGGGCCACAGTAGTCCCTCTCAGCCTTGCCCTTAGTAATGCTACACTGGGCATTTAGCCAAAGGGGATAAACAGTAGCATCTGAATGTTCCCTCGTCCAAGATTCTGACCCAGAGCCAAGAATAGAAACAGACAACAGTGGATAGGCCATGTCCCACTGAGGCTAAGGAAATGTTTATGTCCTTGTCACCTGTCTGTTCAGCCAACCATCTCAAGAGCCTAAGCATTCTCTGCCTCCTTGCAG
Seq C2 exon
GGAGAAGATGGCTTACCAGTCCAAGGCTGCTGGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000552:ENSRNOT00000046537:35
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(40.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.0=53.8)
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]