RnoINT0040234 @ rn6
Intron Retention
Gene
ENSRNOG00000010663 | Col6a5
Description
collagen type VI alpha 5 chain [Source:RGD Symbol;Acc:1565804]
Coordinates
chr8:114578349-114582045:-
Coord C1 exon
chr8:114581992-114582045
Coord A exon
chr8:114578385-114581991
Coord C2 exon
chr8:114578349-114578384
Length
3607 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CTTTGCCTTTGGTGTTTCAGGGA
3' ss Score
11
Exon sequences
Seq C1 exon
GGGAGACCTGGACAGAAGGGGATAGATGGCAGTCCTAACTCCAGAGGAAGCAGG
Seq A exon
GTAAGTATGTCCCAGATATTTCTTTCCCTCCTTATTACTTGTGATGGACTCAGACATAGAGGCAGCAGACCTGTGGCTGGTAGGTACATTTGCTGGCATTCTAAAATCTCAACACGACTCACCTTTGGGGCCTGAGAATTACTTCTTATGTAGGACTGTCCTGCACCTTTTAAGATGTTTTAGCAAAACTCCCGAGCTCTGCTCATCTGCTGACCCATTTGTGACATCCAAAAATATCTTTTCAGAAATTGCCAAATGTCTACAGCTGGTGGTTGTGGGATGCAAAATCATCCGTGGTTGAGAGTCACTATTCTCTAGTGTGCCTTTGCCTTTTAACCTTTAAGGTGTTTCTGAATTCCTTTGAAGAGAGTCCATGACTTGAACATACATGCTCTCCTCTCCTAACTTAGCATCAGGGAGCTATATCAGAACATCATGGACTAGGTGGACATAATCTCAAGGTCTTACACATTGACAGTGTGAAGGGAGAACAGGAGTGGCTTCTTCCTGAATGGACTCCCAAACCCTGGCTATTAGAACCAACAATGGCAGCCAACTCATTGGGGGCCTTGGGGTAGCTTATAGCAACCACAGATGATTTTTGTGTGTGTGTGTGGGGGGGGATCCTGTTATGTACCCCTGGCTGGCCTGGAAGTCACTATGAGTAGACCCGGCTGGCCTAGAACTCATCCTGCAGATCAGACCAGCCTCAAACTAACAGAAAATCCTCCTGCCCCTGCCTCGTGTGTGCTGGGATTATAGGTGTGCCCCACCACAACTGGCAGAGAGATGACATTTGTATTGAAAACTCCTCTGTCCCATACTCAGCATGGATGTAATAACAGAGAAGAATGTTCAAGGCCTGGGTTTGGCCCCAATTTGTTCGGAGGGAATGAAAATACTTGGCTTTCTTTTCTGAGCGTTGGATGGTTCTCATCTCTTGAAGGCGACAGCCTGTTGCCCTTTTCCCTGGGAAAAGAGGCTCCATCCTAGCCCTGTCTTGCCTTTGTTTATCCTGAATGGTGAAGATCCTAAGCCAGAGGGGCTGGGCTTCCCAAGCTTCCAGGACCTTTCCCTAGGAATTGTGCCTTGCAGACTCAAGAGGATTAAGATGTAATTGTGGGAAGGCAGCGGAACTGTGAGATGAACTAAGTGTTATAAATTTTAAAGATAAATATATCTGTTGGCTCAAGAGAAAAAGGAGTTTAGTTTGAGAAAGGTTTATAACTGACACATAAATCATGCACTTTAAAAACAAGAGCAGTTTTGGGAGCCAGGGAAGGGATTAATCCTTGGTCATGCTAGTCAGTACCTTTTAAATCACTGTAAGGACAGAAGGACCTCAGCCTCGTCCCAATCCCTATCTTTTACCTATTTCCCTGCTTTGAATTTTCTTTTCTTTGGAATTAAATAAGGCAACATTCATATTCATGTTCATAATCAAGCAACCTGAGGCTTTTCTACCCCCTCCTCCACGTTTCCAATGTAGGCTAGAATTCTGTTGTGAAACAAAAAAAAGATTTATTTATTTTTCATATATGTGAGTACACTGTCACTGTCTTCAGACACACCAGGAGAGGGCATCAGATCCCATTACAGATGATTGTGAGCCACTGTGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCGCCCCTTGATTCAGAGCATCTTAAGTGGATAATGGATTGAAAGCAACACACCCAACCCCAGGCATGGGCTCCCCAGTGACTGAACTTCAACCTACATAAATTAATCATCACAACAGCTGTTACTAAAACAATGGCTCAACCTACTGACAACCACACAGGAAGCCACATTCCAGACCCATGACCTTTGGCAACCATTTGCAAAGAGTCTTTATAACCTTTGTACTTCTAATATATCATCTGTTATGTAGCAGTTCCTCATCTAATCACTTTTAAATACTCATTTAGATAAAACCTCATAAGACTCCTGACAGGTGGATTATAGCATCATATCTGCGTTAGGCACGGACAAGTCAAGGAGGCTTGGGCAACGCCCTAGGTCACAATAACTAGTAAGTAACTGAGTAAGTGAGCTCAGCTGCTCTCACTTTAGAGTCTATGCTGCTAATGACTGTGTGAGGCTCACTGTGGATTTTCTTTGGGCCACCTGGGCTTTAAGTAGTGGGCCTGAAGGCAAGAGGCCATGCCTCTAAGGACAATGTTGTACAAAAATAATTACACAGAATAAACATTATTCTTCCTTTTGGCCTTTCTTCTCTACACATCTTCTTTTCCCCTTTAGCTCAGGCTGACCTTGAACTTACTATATAGACCAGACTTGTCTTGAACTCAACCTCTATGTGCCTTGGCCTATCAAGTGGTGTGATTGTAGGCATATGCCATTGTGACCAGCTTATCCTTCTTTTGTTTTTTACTTGTGTGCATGTGTGTGCATATGTGCATGTGTGTGCATATGTGCACCTGTATCCAGGTACCCATGGAGGCCAGAAGAGGATGTTGAGTTACAGGTAGTTGTGAACCCCCTGGAGTGGGTCCTCTGCAAGAGCGGAGAGCACATTTAACTGGGAAGACACCATGCTCGCCCTTATCCTTGCTTTTTGATGGAGACAGAATGTGAAGTTCTGCCAAGAGTCTCCACCTTCTATGGCTTTTCAATCTTCTCTGTTTCCCTACATCAAGAGCATTGACTAGTCATATCAAGAGACAGACAGCTGATGAGTTACTATGGGTAATTTCTCCCCAAATTACCAAAGGGTATTTTAAAAATTTAATACCTGATGGAGAGCATAGCTGGGCAATTTAATCTAAGGAATTGTAGGAGGTGGGCAACTCGGAGAAGATGGCGGTTCTGAAATAATTCCTTCATAGTAATCAAATAAATGCAATTGTTTAAAATAATTGTGGTTGGTTATCACAACACAATATGAGTTGGTGGTTAAGAATGTTCCATGGCTTCTTCAGTGAGAGTAATGCCAGCAGATTTTTATCGCTGTAGTTCTCAGAAAAATAAGTTATGGTCTGGGGTCCAAGGCATTGTCCCTCTTGGCTCTTCTCTGTCCCTGGAGCTTGCACTGGCAACAGAAATGGCCTCCCAGAGAAGTACAGACAGAGCTGAGGGACCAGCCTGGCTTTATTGTGATAAACTTAATCAGTAGCATCGAGATCACACAAAGGAGCAGCCGCACCCCATGGGATTCTCCAGTGTGGGGCCCACGTGATGCATCGAGTGACATACCCACAATGTCTAGAAATTTCACTTTTCCCTCTGCTCGGCACACAGTACTTCACGGGTTTGCAGGGAAGAAAATAGTCTTCAGGGTGATCTGAACCCCCAAATAACCTATTTGATAACCGTCAGAGAGTATCAGACTGGGGTGGAGGCCGTAGTGACTTTACATTGGGTTGCCATCAGTTCTCTAAATGTTAATGTGATTAAAACATCCAGTGGGAAAGCCTGCCCTGTCAAGGCCCCCAGAGAACCCTCTATGAGCAGGGAATGGGGGAGACTGGTTTGCCTCAGAGACCGTCCTTTTGTCTGGGCACACTGACTGATGCTTTGCCTTTGGTGTTTCAG
Seq C2 exon
GGAATGCAAGGCCGGAGGGGGCCCCCAGGTCCTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010663:ENSRNOT00000038160:19
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=PD(14.0=66.7),PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(12.6=100)
Main Inclusion Isoform:
NA
Other Inclusion 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]