RnoINT0039649 @ rn6
Intron Retention
Gene
ENSRNOG00000058560 | Col2a1
Description
collagen type II alpha 1 chain [Source:RGD Symbol;Acc:2375]
Coordinates
chr7:139475883-139476625:-
Coord C1 exon
chr7:139476548-139476625
Coord A exon
chr7:139475928-139476547
Coord C2 exon
chr7:139475883-139475927
Length
620 bp
Sequences
Splice sites
5' ss Seq
ATGGTAGGA
5' ss Score
6.66
3' ss Seq
GTTTTTCTGTTCCAATGCAGGGC
3' ss Score
9.61
Exon sequences
Seq C1 exon
AACTTTGCAGCCCAGATGGCTGGAGGATTTGACGAGAAGGCTGGTGGTGCCCAGATGGGAGTCATGCAAGGCCCCATG
Seq A exon
GTAGGACTCCAGTTCTGTGCTGCCCACATTGGGGGAGGGCACCTTTCGCAGAGCCAGACACCCAGCGACCTCCGCCTTGCAGATGTCTTGAAGCATCTCACTCCGGCTACGTGAAGCCTCTCATTTAGCCCCAGGAGTTTGGGTTTTCAGGGTGATGGATGCTAGTCTTGATGATGCTTTAGAGGGGCTAGGAAGAATGAGGACGGGGTGATGCGTAGAGCTGATGGATTAGAGGGCCAGTCGACATTGCTCTTGGAAGGGGAACTGAAGAATGCAGACAGCAGCTACTGTTCTCCAGCATCCACCAGGCTTCCAGCAGGAAATCTCACCCTGCGGGGCTGGCTTGGCACATGCTAAATGAAATTCAGACTTTAGTAAACATGGCCGCCGGCCAGGAGAGAGCAAGGCCAGCATCTCTGTCCAAATGGGGCCTATAAATAAAGATAGGTGGTTGAGTGGGGAGTGGGGAAAGAAGAGGGAGCAGCCGCTGGAGGCCCTCCGCCCCTCCCCCTCCTGCTCCCATGCTATCTTCTCTGTCCTTTTGCTGGTTAGAAGATGGAATCCCAGAGGCCCATGATAAAGCAGGCCAGTAAGCATCTCGTTTTTCTGTTCCAATGCAG
Seq C2 exon
GGCCCCATGGGACCTCGTGGACCCCCAGGCCCCGCCGGTGCCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058560:ENSRNOT00000086062:7
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(0.1=0.0),PF0139113=Collagen=PU(6.5=15.4)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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]