RnoINT0038861 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216934013-216935261:+
Coord C1 exon
chr2:216934013-216934075
Coord A exon
chr2:216934076-216935219
Coord C2 exon
chr2:216935220-216935261
Length
1144 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGT
5' ss Score
9.09
3' ss Seq
ATGGCTATTTTCTACTACAGGGA
3' ss Score
7.2
Exon sequences
Seq C1 exon
ATCAATGGCCATGGCGCATATGGAGAGAAAGGGCAGAAGGGGGAACCTGCTGTAGTTGAACCC
Seq A exon
GTAAGTGCTTTGTAACATGTCGTAAAGATTGCTACAATTGTCTAATTGATGAATTGCCATTAAGTCATTATATATGACCATGCATTTTCAATGAAAACTCTGGTGTTTATAATTTTTCACAAACAGGTGTGTGGGCTTTCTGGAAAGCAAAATTTCAGAAAAATAAAATTATCACACGTTTATGTAATTTAGAATTTTGAAAATGACTGACTTTCTTTGGTTCAATTCTTTGTTTACAAATCTGAATTTACACATTTTATTCTTTGATTTCAAATGTTCGGTGGTTGAGATACAATCGCTTTAGGTCTTCAGTCTGTGATTTTATGGATAATTTATTTAACTGTCTTATTAGAAATATCATCTGAAGTACATTAAATAAAGTGAAATAAGTAGACATGGCCTTGAGAGAGAGATTTGTGGAGAGGGCAGTCAATGGAAAAGTGTAAAGGAAAGGGAGCAGTGACTGTGGACAGAATGTATGGCGTTTTCTTGTAAACCCATAAGACCAGAATATTCTCTAAAACTTCATTTTGTTTACTTGCATGATTATGTGGAACTATAATTTGTATTAAAGCTATGAGCTCTGAAGATATTGTTAAGAGAGAAGCAATTAAAAAAATTCATTAGCCAGTAACATGGAGAAAGCAGAGTGTTAGGACTGTAGGCTGGCTGTTTAACTGTTCACTTATTAATCCTTTCAATAATCACAAAGAAATACAGTTTTGTGGAGTTAAAGTATTTAGGTATTATTTCCTTTCATTGGTTTATTCCTCAATTCATCCACTAACACGGCAAATATTTATCATGCTCCTGTTTTCTGTTTATTTGTATTTTGGTTATAAATTAAGTAATTAAGTGCTAAGGAAGAGCTTGATGAGACATTTCTGCTGTACTCTCTACAGAAGCACCTAGAATATTCTTTCTCCTTCCTAATATCATTTGTCTGAGTATCTATTTTACTTTCAATTAGTTCGTACATTCACTAATAGCATGATGGAAGTTATATCTTCTATTATTTTAAATTATTTTCTTTTCCCATAGAAACATATTTTGAATGTTTTATATCATATGAATTTAGACTTGACTTTAAAACTATTATAGTTGGTGGAAAGGCTAAAAGTTTCATGGCTATTTTCTACTACAG
Seq C2 exon
GGAATGCTTGTTGAAGGACCACCTGGGCCAGCTGGACCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:9
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=PU(1.7=4.8)
A:
NA
C2:
PF0139113=Collagen=FE(22.0=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]