RnoINT0040268 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114417265-114419823:-
Coord C1 exon
chr8:114419797-114419823
Coord A exon
chr8:114417310-114419796
Coord C2 exon
chr8:114417265-114417309
Length
2487 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
AATCACATCTGCCTCTGCAGGGT
3' ss Score
7.61
Exon sequences
Seq C1 exon
GGAGCCCGAGGACTCAGCGGAGAAGAG
Seq A exon
GTATGGCCCTTATTCACCCCTCAGTTATCCAGAAAACTTTGAGCTTCATTTTTTTTTGTTTCTTTTTCTAAAATATCATTAGAGGATGCTACAAGTGCAGCCACTGTTAGCTTTCCTTTTGTTTGTTTTTTGTTTTTTGTTTCAGTACCAACTATTTCATTTAGTGTTTTTTTTTAAAAAAAAACTGTTTGAGATTCTAATTACAGTATTTCTCCTTCCCTTTCTTCCATCCAAACCCTCTCATATAATGTTCCTTTTTCTCTCTCAAATCCATGGCCTCTTTTTTTGTTGTTGTTAATTGTTGTTGCAGGCCTATATGTACATGTACGTAAATACAGCCTGCTCAGTCTGTATAACGTCCCTTGTATATATGTTTTCAGAGTTGACTGTTTAATGTTGAATGAGCAGTTGATGTGCCCTTCCCTGGGGAAGACTATTTCTCTTGCTCGAATTCTTAGTTGACTACAGTTCTTTGTGTAGGACTGCGGACTCTTCCCATTCACCCTGACATTTCTATTGCCCTTACCCTGCTTTAACTCATGTTTATGAAATCATGTTGGTGAGACTTTGAGTGTAGCTTCTGATGTTGCTAGGAGACACAATCTCACAGCAAACTCTCCAACCTCCTGGCTCTCACATCCTCCTTTCCCTTCAACGATGTTCCCTAGGCCTTAAGTGCCAGGAGTGTTTTGTTAGGTGTATTCATTATGACTATGCCCTCAAACTCTGCATTTTGATTGGTTGTGACTTTCTGTACTGGCCCCTGTCTTCTGCCTCTGTCTGTTGCCACAAGAGAAGTTTCTTTGATAATGGGGGAGGTGCAGGGAGTATATTTGCCTGGGGTATGAGGACAGATGTTTAGACTAGTATTTGGGGGTTGCTGGATTAGTAACATTGTGGGTTCTCCACCAAGATCCATGACTTCACTAGCACTGAGTCTGGCTAGGTTTCAAGTACCATGTTTTCATTTTTTGCTGAGCAGGTCTTAAGTACAGTTATGGAGCTGTAGGTTACCACCAAGGTATACAATGCCACTACTGCACCCTTAGGATTCTCGTGCCATGCTGGCGATGGTGGTTCACAGGCATCATAGCTGGCAAGGACAGTTGGTTGCCTCCCTTCTTTGGAAGCTTACATGGTACCTTCTGGAACCGTGAAGGCTAGTCCTCAGGGAGGATGCATTCAGGTCAGTTCCAGTTCTGAGTCTCTGGGCTCTGGGTCTGAGATGGATGGAGTCAATAGGTCCACCTCTGGGGGAGCAGTCAGGGACAATAGCAATAGGCTGTACATTTGGGGTCTTCTGGACAGCCCTGGCCAATAATTCAAAAGAAGGCTTCTTGTATCTGGTATTAGGTTTATTTTTAGGTGGTCTTCGGCTCTTGCATTGTCAGCCCAGGTAAGAAAAGTTCACCAAAACTATATATTTATATTTATTCACTGAATCACATGCATTATAGGGTCATCTTGGTAAATAGTTAATGATTCCTTAAGGCCTTAGCAGACATCCATATTGGTATTTTACCCACTTCCCTCCTCCTTCTGGATTTTCTTTCCTACCACTCCCTACAGAGCCTCCCTTTGCCCATTTCCCCTATTGGATGCCTTGTTCCCAGCTCCCCTCTTTGCCCTCCTCCCACCTTCTGTATTTGCCTCCCCCCCCCCAAGGAGTCACATTTGCTCCCGTTTCCCTAATCAGATCGCTTAGACCCTGCTATTGCCCTCCTGTTCCTCAACCTCCCTATCCTGGCAATGTCCCATTCTACTCTCCTGGGTCCTGTAGTCACTCCAGGCTACACACTCACATCTGAAGACTCTGAGTGAGGGGCCTCCAGGGACAGAGAACACACAGTATGTTCCTTTCTGGATCTGGGTTAGCTCACTCGCTAAAGGTCTCTGCTGGTCCCGTCAGTCCATGCTGTCATTCGTCTTCCTAGATGAATGGAATTCCACCGTGTGTACGCGCCACAGTTCCATTATCAATTTGTCAGCTGAAGGACATTTACGTTGTTTCTCTCCCCTAGTCGTAAGCACGGCTGATCTAGTAGCTGTGGAGTTCGATGTCCAGTCCTTGGAGCACGCACCAAGGTGGTATAGCTGGGTAGCATATGGTAGATTTATTTTTAGCCTTTCCATAGTTCACCACGTGGATTTCCATAGTGACCGCAGCAGTTGGCAATCCCAGCAGCAGCGAATGAGGCTCCCTTTCCCATCATCCCCTTCGGGCGTTTGTTGTCCATCGTCTTGTTGGTATTTGGCGTTCTGACTGGGGTAATCTGAACTCAAAGTTGTCTTTACGTTTTACCTCTGCCTCTCCTATCGGGCAGGCTCCGTTCGTTACGGCAGCTTCTGATACTGAAACTGACCTTCAACATTACCCAGGTGTCACCTAACAGGCTGTTGCTCATCACGTGACCCCCAAGACTGCTTTTGGTTTTGGTTTTGGTGCCTGACAGATGTACTGTGTTCTAATCACATCTGCCTCTGCAG
Seq C2 exon
GGTGAAGTTGGGGAAGATGGGCTTGACGGATTAAATGGAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:14
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(1.7=11.1),PF0139113=Collagen=FE(11.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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]