RnoINT0038973 @ rn6
Intron Retention
Gene
ENSRNOG00000000552 | Col13a1
Description
collagen type XIII alpha 1 chain [Source:RGD Symbol;Acc:1595704]
Coordinates
chr20:31485230-31487005:-
Coord C1 exon
chr20:31486952-31487005
Coord A exon
chr20:31485275-31486951
Coord C2 exon
chr20:31485230-31485274
Length
1677 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
TCCCTGTTACCATGCAACAGGGG
3' ss Score
4.54
Exon sequences
Seq C1 exon
GGAGAAGCTGGTGTCGATGGACAGGCTGGTCCCCCAGGACAGCAAGGAGACAAG
Seq A exon
GTAGGGCCCCCCATCCACCCACCCAGTCAGGAGCTGCAGGACGAGGGTGATCTTGGGGGTCTAACACAGCTCGGAGAGCCAGTCATCCCTAGCCTGACTGGGCCACAGTGCTGACCCCGAGCTAGCTAGCTACAGTGCCTGCGTCCCATCTTTTCAGAGAAGCATCCGCCGAGACAGTGATCCTGAAAAGCTGCTTGGAGACCGGGACGCGTTAGCTGAGGAAGGAGTCTGAACTCTGGCTTCTAGTAGCTTCCCGCACCACAGATCTAGGCAGAGAACCCCCTTCTGCCCCTGCCTCCTTCACAGGCACACGATAAATGAACTCCTGAGGTGGGAGGGACAGGGGGCAGATCCTCAGAGGGACAGTGGCAGGGTCATCTGAGTCGAGTTGAGAGCATTCGGTTTCCCTTCATCTTTGACTTGGTATAGGAGTCAGGGTTCTCTAGAGTCCCAGGACTTAAGGAATGTCTCTGTATATGAAAGGAAATTATTGACATGACAGTCTGCAGTCCCAACTAACAGTGGGCAGCTGTGAATGGGAAGTCCAAGAATCTAGTAGTTTCTCAGGCCCATGAGGGTAGATGTTTCAGCTGGTCTTCTGCGTAAGCTGGAATCCTGACGAAGTAGGCTCCAATAGATGTGCTGGCAAGGGAGTGCAAGCAGGCAGAGAAGAAGGAAGTCTTCCTTCTTCCAATGTCCTTCTGTAGGCCTCCAGCAGAAGGTGTGGCCCAGATTAAAGGTCTGCACGCTTGGACTTAAGCTGTTCTTTACTTGGAACCTGATCTGTCCCAGGCTGGCCTTGAACTCAGAAGTCTGTTTGCCTCAGTCTCCTGGGATTAAAGACATACACCACCTTGCTGGGACCTAAGCTTTTCATGGCCACTATGTGTCAAGGTCTAGATCACGGGTATGCCCTCCATTTCTGGATTGTAGTTCATTCCGGATGCAGTCAAGGAGGTACTGAGACTAACCATCACACTGGGTGTTCTGTCTTTAGAGCTCACATTATCCCCTCCCCCCCAAAAAAACCAAGGTGTGTGGTTTGTACTTCGCTTGATACTACTACCCCACTTACTCCATATTACCTGGTCCTGTTTCCAATAGGAACCACCTCCAGCCCTGGCCCACTCTAAGACATCAGTATCCCTTCTAGCTGCTCCGTCCTGACACCCCTGGCCTCTGGGTTTCACCCTGTGCTCCCTTCTACCCCAGGGAGAATGGTCCCTGAAAGGACCGTATGGGTTCCCTGTGGCCATCACTCAACAGTGGGCAGCGGGCCCTGCTGCCAGTACAGAAGGGAAATCAGAAGAAGCAGGGGCTAGATCCCTGCTACCAAGGACGAGACTGGACTGGGGAACTGGGGGAAAGTGGCCAAGGGGACAGACAGGAGTCACCAACAACTAACACAACAGAAAAGAAGGGACATCATTAAGTGTAAAAGGAGAACTGCAAGGTTCTTGAAGTCAGAGGAACGAGAGTGGGGCAGGTGTTAGGGATGTTTTTGGAAGGGAAAGGGACCAGTGCTGAAATAAACAGGAAAGCTTGTGTTCTGGTGGCTTGTGCCAAGACAAATGAGCTCCTTGGCCCCTCCGTGGCCCTCACAGTGTAGCTCCCCAAGGACATTGGGTGTTCTTGAAGCCAGCCTTACCAACCCATTTCCCTGTTACCATGCAACAG
Seq C2 exon
GGGCAGCCAGGAGCAGCTGGCGAACCGGGACCAACTGGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000552:ENSRNOT00000046537:19
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(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
Main Inclusion Isoform:
NA
Other Inclusion 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]