RnoINT0038970 @ rn6
Intron Retention
Gene
ENSRNOG00000000552 | Col13a1
Description
collagen type XIII alpha 1 chain [Source:RGD Symbol;Acc:1595704]
Coordinates
chr20:31488627-31492105:-
Coord C1 exon
chr20:31492073-31492105
Coord A exon
chr20:31488672-31492072
Coord C2 exon
chr20:31488627-31488671
Length
3401 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TGTTCTCCCCCTCCTTGCAGGGT
3' ss Score
13.21
Exon sequences
Seq C1 exon
GGTGCTCCTGGGATTGCCGTGGCTGGGATGAAG
Seq A exon
GTAGGTAAAAACCCTGTCACTGTGTCAGAGGCAGGATCAGATGGTGTCAGGAGACCACAAAACAGGGGCTCGGGCTTAGTAGTGTCAGAGCTGGATCGAGGGGAGGACAGATGTTTCAGTCTCCAGACTCCACTCAGGGTCTCTCAGTCTGCCCCTGAGAGAAGCCTGCCCTTTCCTGTACTCCAGAGCTAGCTGTTGTGGGCTTCCAAAGACTCTGAGAGGAGAACCAACATCTTTTCCCTGAACCCCTAACCTAGACAAGGGCTACCCTAGCGGGACAGATGCCCGATGTTGATCTTTACAGCAGCTCTACTCACCTGAAGCACCACCCCTGAGATGCTTCAAACCTTCCCATCCTTCTAGGGCAGTGTTTCTCAACCTGAGTCGTAACCCCATTGCCGGGGAGGGGGTAAAACAGCCCTTTCACAGGGGTCACCTGAGAACCCCCCCAGAAATCACAGATATTTACATTACGATTCATAACACTAGCAAAATCACAGTATGAAGTAGCAGCAAAACTAATTTTACGGTTGGGGAGCCACTCAACGTGCAGAACTGTACTGAAGGGCTGCGGCATGAGGAAAGTTGAGAACCACTGGTCTAGCGGGGAAATGAGACGCTCAGGAGCCTCCGTCCTGGTGTTTCCCCTCGGCAGAGGAAGTGCCCCTCCTGGAAAGCAGAGGGCTCTTGTTCCTGCTTTGTCTGTTTCTTCTCTGCCATCTTCTTTCCCACACAGGGTGAGCCAGGGACGCCAGGAGCCAAGGTACTGGTGGAAGGGGAACCCTGTGGGGGGCATAGAGAAATGAGATTGGCTGGGGGTGAGGCCGACAGGGATCACCATTTTCCTTCTGTTCCCCTTGGGGCCAGCCGTATGAGCTTGCACACGTGCATACATCTGTATATGTTGGGGGAGCTGGCTAAGTCCTTTCACCAGGAGCACACTGCAAAGACTTGCCTTGTCCCTGGTGCTGCCTGTACACAGGCAGGGCAGCTGTGGGGCGGGGGGTGAGAGGGAGCGGGCATGACACAGTCCCTCCCCTGCACTTACAAGTGTCTCTTCTCTACAACAACAAAGGATTTAGCGTGACAGAAATGTCAGACAAACTTGAGAAAATTTGGAGCCAGGCCAGGTGGGCACAGGCCTAGCATCTTGCCTTCTTTAGATGGCCAAGGCAAGAAAGTGGCGAATCAAGTCAAGCCTGTTGGACTTAGCAAGACTTTTTCTCCAAGGGAATGATGTAAGAGGGCTGAGGATATAGCTCAGTGGTAGTGTATTTGCCTGACACACAGGAAGCCTTAACTTCAATCCCTGGTACATCGGTATCTTTGATGCGAGCCTTGGAGGGTGGGGAGGGGGATATGCTGCATGTGCACTGGGAAATCCTTAGGACCCTATAAGTAACATCTGTGTGTTCACCTGAACACCTCTGTTTAAAAGGAGCCTGAGAACAGTTGTCTGGGAACCCTGGCCTCTGATTGCACCTCATCCTCCCTTCCCTGCCCTGTCTGCCTATTGGTGACTTTGTCCTCTTCTCTCTAAGAGAGAGTCAGGGAAGCTGGGGCTACCGGGGCACTGGGAAAGAAGGACAGAGGAGAGGGCAGGACGCCTCAGGGGACACTGGCCTCGGGGCTCTACCATGTAGCTACTGTGCTGGACAGGAATGTTGTGGAAGAAAGGAATGTGGTCTGGAGCAGCAGACCTGGGGACACATACCCCTTCAGAAGTCTTCAGCTCGCAGTGAAAGGCAAAGGGATCTCAGCATCTTTGGTACCTTACCAAGCATCCTTGCAGATAGGACCTGCATCTTTTGCTGCTGCTCTTGGGGATGTCAGGCTAAAGCCCACTCCAGTGCAGTCACTGACTCTATTTACCAGGCTCCTGCCTGGCTCTCTCTGCCTCCTTACTGCATCCATGGCCATGTTACCAGACAGCCTATACCCAAGAGTAAGCGGCAGGGACATGACACCGAGAGCCACCATGGTATTATTCATGGCTCCAGATGGAAAGATCATTGACGTCGTAGCCCCCAGAACTCCCAGATCATTTTCTTGGATGTAGGAATGGCATTCCCATGCTCAGCACTAGGAAGGCGAGGGTTCTAATGGCAGCCCGAATCCGACTCCCTGCTGGTGGGGAGCACTGGCCACTGAGCACTGCTGTGGACTGAACTGTGCCCTCCCAAATTCATAGGCTGAAGCCCTGAGCCCCGAGGGGTCAGAATTAGAGAGTAGGGCTTTTAGGGGACAACAAAGGTTAAATGAGGTCGCACCAGTGAGACCCTAATCTGACGGTGTTGGTGGCTTCATTAGCAGAAGAGAGATAGTTCTCCTCTTTGACAAGTGTGAGCCCTGACAAAGGCAGCCATCTATAAACCGAGAGAGCCCTTCCCTTCCTCCTTGCTCAATCGGGCACCCAGATGGCAGACTGCTCTCTCGGCTACCCTATGACACACGTGCCAACTCACACAGACACTGTGGAGGCCAAGAGAGGACTGTACCCTACTTGGAGGACTATGGGAGACTGGCTCTGCCATTAGCTGAGTAAGCGCCCGTCTACAGCCAGCTAGATCATGGGGTCGACCTGCTCCACCTGTGAAAGGAAGCTTGGGTTCCTCTAACCCTTCCAGAACTTAGTGATTCAAGCCCTGGGGTCCAATAGCCGAGTTCCTCGATATTGGACAGGGCTGGGGCAGGGAGCACTGCACCAGCGATCCACAGACCAAGTGTATTAAACAGTAAAACTTGCATTCTCTCTTGGCCCACAAGGCCAGAAGCCCAAAGGGAGGGGGAGGAGGGGAATGCGGTCTGAGGGCTTTTGCTTCTCGAGTGGTTTATGACCATCATCACACTCCTTCACCTCATCTGCCTCACATAGCCTCTGTCTGTCTGCTGCCAGTCTCCTGAGAGACGGATGGGCAGACTTCTTGTCCTAGAAACACTGGGTCTTATCTACTCCAGCACGATCGCTTTCAGATTTGATCTTAATTGATCTTCAATGACCCTCTTCCAAAAAAGGGGTGGAGGTCATTTTCTGATGTACTAGAGGTTAGGACTCCAACACCAAACTTTGCTGGAACACAGTTTGGCTCATGACACGAACTTCTCAGAAAGGGCGTTCTGGTGGATGGGTTCTGTCTAAAGGCAGGAAGACATGGACAAAGGAGACAGGCTCATTGCGGGGGGAGGGGAGGCAGACAAGAAGAGTGGGTCAAGGGGGAGTTCCTAAGTGCTCTTTCCATACCTGCTTCCAGCCCACTCCCACTCCCAGGACTCAGCAGTAGACTTTGACTAGTGTGTGTTCTCTCTCCATCCAGGGGAGCAATGTGCTAAGAGGGTAGGGGTGCTGCCTCCCAGACATCCTGACAAGGTTGTTCTTAACCCTGTTCTCCCCCTCCTTGCAG
Seq C2 exon
GGTGAGAAGGGTGCTACAGGCTCCCCTGGCCTCCTGGGGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000552:ENSRNOT00000046537:16
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=PD(10.3=54.5),PF0139113=Collagen=FE(15.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(22.2=100)
Main Inclusion Isoform:
NA
Other Skipping 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]