RnoINT0040291 @ rn6
Intron Retention
Gene
ENSRNOG00000023007 | Col6a6
Description
collagen type VI alpha 6 chain [Source:RGD Symbol;Acc:1309172]
Coordinates
chr8:114441224-114443082:-
Coord C1 exon
chr8:114442522-114443082
Coord A exon
chr8:114441782-114442521
Coord C2 exon
chr8:114441224-114441781
Length
740 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
TCCCAGTTTCTCCCATGCAGCCT
3' ss Score
7.27
Exon sequences
Seq C1 exon
CCTGTGTGGACACAGAGGAAGCGGATATCTATCTGCTCATTGATGGTTCAGGGAACACGCAGCCCACAGACTTCCATGAGATGAAGATCTTCCTGTCCGAGGTGGTGGACATGTTCAACATCGCTCCCCACAAGGTGCGAGTCGGGGCCGTGCAGTACGCCGACACCTGGGACCTGGAATTTGAGATCTCTAAGTATACTAACAAGCCTGACTTGGGAAAGGCCATCGACAACATCAGGCAGATGGGTGGAAACACCAATACGGGTGCAGCCCTGAACTTCACCCTGACGCTGTTGCAAAGAGCAAAGAAGCAACGGGGAAACAAAGTGCCATGTCACCTGGTTGTCCTGACAAACGGCATGTCCCAGGACAGCGTCCTGGGTCCCGCGCATAAGCTGAGGGAGGAAAACATCCGTGTGCATGCGATCGGCGTCAAGGAAGCCAACCAAACACAGCTGCGGGAGATAGCGGGAGATGAAAAGCGAGTTTATTACGTGCATGAATTCGATGCCTTGAGGGACATAAGGAACCAAGTGGTTCAGGAGATCTGTGCTGAAGAAG
Seq A exon
GTAGGAGATGACGTGGCTTGACCTTCAGACAGCAGCTCACCAAGGGACACTGTTAGTCTAGATGGATGGCCCACTTTTCTTAGTTGAGATGTTGGCATGTGTGGTAGCAAAATCCCATTGTAGTATAAATTAATATTGGAAAAAGGACAGCTATTTAGAGGGTTTCTCTCTGAGGAGTATTAATTAGCCTCTCTCCCCACAGACCCCTGCTAAGATGTATTGTTAGGTGTCATGTGTATAATACAATCAAACACGTTCCGAGAAGGAGTGTGGCTATCTGATGGACATTTCATTTTACAAATGAACTTGTCTAAATGTCTCTGGAGTGCTGTATCAGTAATTTTCCACACATGTTTTTTTTTTTTTTTAACTATCCGAGAGTACTTGGTAACTTGTAGATAATATTTCTGGTATCTTAAGTAGGGATCTCTCTCGGCATTACCGAATGGATGAAGCCAGAATGTTTGCTGGCCATCTTTAAAGATTGACAGACAACTCAGAGTACTGCTACAGTAAAAATGACCTGGCCTCAGACGGTGCCAAGATTGAGATGGTTGAGCAAATCACCAGCGAACAGAATAACAGTCTTGGCTTTTATTGCTTGTGATGCTTCATTTGCCTAGCTACCCTCATGGTGCACACACTGAGCTTGAAGTATTTGTGATCTGGGTTTTCCTGTGAACTTCTAATTTTTTTTATATGCCTCGATGTATGTAAACATCCCAGTTTCTCCCATGCAG
Seq C2 exon
CCTGCAGAGATATGAAAGCGGACATCATGTTTCTGGTGGACAGCTCTGGCAGCATTGGACTCGAAAACTTCAGCAAGATGAAGGTGTTTATGAAGAACCTGGTGAGCAAATCCCAGATCGGGGCTGACCGGGTGCAAATTGGTGTGGTCCAGTTCAGCCACGAAAACAGGGAGGAGTTTCAGCTCAACACATTCATGTCTCAAAATGACATTGCCAACGCCATCGACCAAATGGCTCACATTGGAGAGACAACCTTGACAGGCAGTGCGCTGACCTTTGTGTCTCAGTACTTCAGTCCTGAAAAGGGGGCCCGGCCCAATGTTAGGAAGTTCCTCATTCTCATCACGGATGGCGAGGCTCAGGACATAGTAAAGGACCCAGCAGTAGCCCTTCGAAAAGACGGTGTGATTATCTATTCTGTGGGAGTGTTCGGCTCCAATGTCACCCAGCTCGAGGAGATCAGTGGGAAGCCGGAGATGGTTTTCTATGTTGAGAATTTTGACATCCTACAGCATATTGAAGATGATCTCGTTCTGGGAATCTGCAGTCCCCGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023007:ENSRNOT00000056414:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=91.5)
A:
NA
C2:
PF0009223=VWA=WD(100=90.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGTGCCATGTCACCTGGTTG
R:
CCGATCTGGGATTTGCTCACC
Band lengths:
358-1098
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]