RnoINT0038862 @ rn6
Intron Retention
Gene
ENSRNOG00000000463 | Col11a2
Description
collagen type XI alpha 2 chain [Source:RGD Symbol;Acc:2373]
Coordinates
chr20:3830164-3833023:+
Coord C1 exon
chr20:3830164-3830457
Coord A exon
chr20:3830458-3832873
Coord C2 exon
chr20:3832874-3833023
Length
2416 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TCTAACCCCGACTCTCCCAGGTG
3' ss Score
6.57
Exon sequences
Seq C1 exon
GCTGGGGTCTTTGAGCTGCCAGGGTGGCCAGGGGCACACAGTAGCGGCCGCCGAGGAGCAAGCAGCACTGACAAGCAGAGGTACCCCCGCAACGGGCACCTTGCTGCATGGAGCTGGGCCGCTGAAAGCTGCTGACATCCCAGGGTCCTGGTTCCGAGGCTCAGCTGGCTTCTGTTTACTGTCAGCACCAGGACTGCCTGGGATTCTGAGCCATGGAGCGGTGCAGCCGCTGCCACCGCCTCCTACTGCTCCTACCTCTGGTGCTGGGTCTGAGTGCTGCCCCAGGATGGGCAG
Seq A exon
GTAAGAGGAGTCCTGCCTGGGTGTCAGTCAGCTGGAGGTTGTAGCATCTGCCTGGAAGGAACCTCTGATGCCTTGGAGTAGGAGCGTCTGAGCCTTAGGAAAGGGATTTGGGCACCAGGTTTAGATGAAGGGCACAACACTTTGGTTCCCTGAGCCAATATAGGACCATCTCTTCCTCGAAATGACTGACGGAGGGCAGGTGATGCCAGCCAACAGGGACCACAGCCGAGAGCCTGAGTAGGCTGGTTTCCTTATTTGGGTCCTCAGAAGGACCTGAGATGGCCAAAGCCTGTTTTCTACAGGCTTCACTGATGTCGGTGGAGTGAATACCAGGGCTGATGGGTAAGGGAAACCGGGTGAACATCTGTAGGTTGGAGCCTAGAAGGCTAGGGAAGAAAGCAACAGCACTGTCCCATCCCCTTTGGGTCCCCCAACCCCTCCCTGTGCCCTGGATGCTGCCACGCGGCTGGCTCTAGGGAGCACAGGGGCTGGCTGCCAACAGGACGGCCACTGGACAGGCCGGGATCAGGTGTCTGAGGCCAGAGCCAACTCTTTGCATTCCTGCCCCTCCCCCTTCAGCCAGCGGGACTCCCATGGGACCCTGGTGTCCACCGACCCCATCTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTACCCCCAGAATGGAAAGGCTCCAAGAAAAGATTTGATAACTGGGTCTAAGCAGGAAGGAACCAGTTCCTCTCTCCTGGAATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTATGTGTGTGTGTGTGTGTGTAGCTGATTTTGTATAGCTCTCCATTATTCATGTTTTCTCTGCTCAAGAGAGAGAATAAGCAGAACAACAGTGTGAAGGATTTAGATTAGGCCAGGAAAGCAGAAAGACGAAGTACATGGTGTTTACAGAGTCTAGGTAGGGGCTGACCAAGGTAACTGTCTCCTATTTGGGAACTGAGTGGATGGAGGAGGGACTCCAAGAAGATGGGTAACTAAGAAGTCCTGAGAGTATAGGACAGTGGGGGCTCAAAGGGATAGATGGAGTGGCAGTGGGTCTAAGACAGTGGGGTTAGTATGTGGCTTGAGGTGGGTGGGCCTGTGAGCACGGTGTGGAACTGTCCTCCATCGGGCTTTGGTGGAGGGTGGGGACCTCCGAAGTCTCCTTTGCCTGGGGTCTCTGTGAGTCTCTGTGTCTCTGTCTCCCTCACCATACTCTCTCAAAGCTGCCCTTGTGTGTCAGTGTTTGCGAAGCTGCCACACTTTGGGGCCAGGCTCTCAGGGGCGAGGGGTGGGGGAAGGTCGCGGTTTCCTCGGCTCCTGGACTCAAAGGGCCTTTTCTCTCCTGCCTGCCCCACCTCATCCACCCCACCCGGCTGGCTCTGCTCTCCTGACTGCCCTGGCCTCTGCCCCTCCCCACACTTCTACCAACACTTTGCAAGCACTCTCAGTGGGAGTTCTCCACTGTGGAAGTGTGGGAGTGAGCTTTCCCTTTCCATCCAGTTTGGGCCCAGGAAGCTGAAATCTAAGGAGACCTGGCTGATGGCCTGCGACTTGAGTCTGGATTCAGGTGGTGGGGGATGGCAGGACAAGACTGAGGTTCCAGGTGTCGGGAGCTTGCCTGAGGTTTGGGCAAGAACTCTGATAGCATCTACAGATGTGTGGCTTGGGGCCCTGGACCTGCCCCTGGCCTGTGTGGAAGCTTCAGTTTCCCCTTCCCCCTCTCTGAACCCACTCGCCAAGTCTGAGGGCCAGGCTTCTGGCCACCTTACTCGTATAGTATATGCCCTTCCTTAGCTCAGGCAGAGTTGCCCCTGCCCCCACCTCAACCCAGTCTCTGTGGCAACTGGAAGATCTCTCTTCTACAGCCGCCTCTCTGCCTCCCCTGTGCCCAGGATGATCGATCATCCAGATGTTGTTTGTGCTAGAGACCAAGCAGATGCCAGGAAGCCAAAGACTGGGAGATACAGCAAGGGAGGGAGAGGGAGAGGGAGAAAGAGGGAAAGAGAAGGGTGAACGGTGTTGGGGAGATGGGCGAACTGAAGAGAGGGTGTGGGAGGGTCCAGCAGGTGCACAGTCGGCAGCAGGGGCAGAGGGCAGGGGAGACAGACTGAGAAGGGAATCAAAGTGAGATTAGCAGAGATTCCCAGCTGAAAGACCCAGATGGCGGGTCTGAGAGGCAGGTGCTGGGAGAAGGAGGGGAAAGAGCATGGAGTAGTTGCATGCCAGCCGGCTAGGTGCACCTCCCCTCTGAGTCACCTTGCCTCCCATCCATATAGGTCCCTTTAGGAGAATGTAAGGGAGATGGAGATCTGGGCGTTCCCCATTTAGACCTTCCTAGTGTTCTAACTCCCAACTCTAACCCCGACTCTCCCAG
Seq C2 exon
GTGCACCCTCTGTGGATGTGCTACGTGCCCTGAGGTTCCCCTCCCTTCCCGATGGTGTTCGGAAATCAAAAGGGGTCTGTCCAGCTGATGTGGCTTACCGTGTGGCACGACCTGCCCAGCTCAGCGCACCCACACGCCAGCTCTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000000463:ENSRNOT00000045533:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
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]