RnoINT0038817 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216965440-216967625:+
Coord C1 exon
chr2:216965440-216965493
Coord A exon
chr2:216965494-216967517
Coord C2 exon
chr2:216967518-216967625
Length
2024 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AATGTTACTTTGCATTTCAGGGC
3' ss Score
8.78
Exon sequences
Seq C1 exon
GGTGAAGATGGCTTTCCAGGATTCAAAGGTGACATGGGTCTTAAAGGTGACAGA
Seq A exon
GTGAGTAGAAAGGAACTTTGCAATATTCTATATATTTTAACACACTGTATCTTTTAGGTAAGGATTCTACTGCTGTGATAAAACACCATGGTCAAAAGAAACTTAAAGAGGAAAGGGTTTATTTTCCTGACAGCTTCAGGGAAAAGTCTGTCGCTGATAGAAGTTAGGGGGGAATCGAGGCAGGAGAGGAACTTGGAGGAAGGAGCAAAAACTATGAAGCTATGAAAAAGTAAAAAAAAATATAAAAGCTATGAAAGACTGCTGTCCACTGCCTTCCTCTTAATAGCTTGGTCATTCTTACTTTACCCAGAACCATTGTTCCTGTCATCCCACAAACCTTTCACATCCATCTTTAATAAAGAAAATACACACCTAAAAGTGCATAGGCCAATCTGGTGGGGGCATTTCCTCAACTGAAGTTCTTTTTCTAGAATGTCATTAACTTGTTTCAAGTCAACATAAATACTAGCTAGCACAATGTATACATATATTTTTCTTAGCATTAAATACAGAAAACAAAGGTTAAGTGAAATATTAGAGACAGTTGACTTTAGTTCTTAGGTAATGAGTGGACAATATGTTTGTAGTGCCAGTGTTTTTCTATGTTCTGTTACTTTTTATAGGAGCATATAAATGTATGAATTTATGTATGTATATAACCTATTGGGCTGCTTTCTAATTAAACCATCATGTTAAAAGTATAGATTTCATGGGGAAAGAACTTAAAACATCTGACTTCCAGTAATTTGACAGATTTGTGTTAGTTGCTAGATGCTTTTATGCAACTATACATTAACTAAATACTCCCTATACATTCTTTTCCTTAAACTTTGCTTTTGTTATTGTTTTAAGACAGAGCCTTGCTTTGTAACCATAGCTAGACTTGCACTCATTATATTGCCCTGGTTAGCATCAAATTCAAAAAGACCACTTGCTTCTGCCTTCTGAATACTGAGATTAAAGACATGAACCACTCAGAATGTTTGACATGCTTGTAAGAAGAGCTATGCTTAATAGAAGTTTCAGAAGGATATGTGTACTAAATGCATTTTCCTAGTGTTGAAGATGTAATTCTGCATTTTGAAAATGCTAGACAAGCATTCTCCTACTGATCTATATACCCAAATACATTTTTGGCAGTCTCACCTCAACAATGGATTCATTAAGCTCTAACCTGAACAGTATCTACTTAAAATCGAGTAGTATTGTTTATGGCAGTTTCAGAATAGCATGATCAAAGGAGTAGAAGAAAGGAATGTGGTTTTATTTTAAATTTTGTGTACATATTATTAACTTTGATGTTTGAGAGCCATATTGTGCAACTCTCATGCATTTTAATTTTTTATGATATTCAGAATTACAGAGTGTAAAGATAGTGTTTTTACACAATTTATATCTGGTAATAAGTTGTTTGGAAATGGATTGACTGACCTGGTATACATTAAATACATTACAGGGAAGATTTATTTTATAACTCATATGAATACACAATCTATCTGATCAAAGAAGCAGACCTCAGAGTAGTTGGGATTCTGTGAAACCCATGTCTGGGGTTGAAACTGAGCTTCTACTGTGTTCATTACATTTTTAAGAAGTCCAAAGGGAAGACTCTTTTGTTCTAAATGATAGATTCCAAAACTGCTTTCAAATCTTTGTTCTTCATTCTTTCTCATCTTTCTCTCCCTTCTTGCTCCTTTTTCCCCTTCTCTCCTCTCTCCCTCCCCCTTCCTCTCTCCCTTCTTCTCCTCATCCCCCATATATGAAACATTCTGGAAGTACACATGGTACCACCAAGCTTCTGCAGCTTTTTGAATATTAGGCCACATTCCGGTATTAATTCAATAATGAAATGCTTGTTGATGTCAAACTACTTCAACCCCCTTTTCAAATGCAAGCATGCGAGCAAACAAAACATGAAGCAACAAACCGAGAGTCATAAAACCTGATTCTCAAATAGACTAGAATCTCTACCTACATCTCTGTTCATGTTTTAAATGAATACACAATGTTACTTTGCATTTCAG
Seq C2 exon
GGCGAAGTGGGTCAAGTTGGTCCAAGAGGAGAAGATGGCCCTGAAGGCCCCAAAGGCCGTGCAGGCCCAACTGGAGACCCAGGTCCCTCTGGCCAAGCAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:29
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=FE(28.3=100),PF0139113=Collagen=PU(4.9=16.7)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=22.2),PF0139113=Collagen=FE(57.4=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]