RnoINT0038800 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216938906-216941830:+
Coord C1 exon
chr2:216938906-216938989
Coord A exon
chr2:216938990-216941773
Coord C2 exon
chr2:216941774-216941830
Length
2784 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGA
5' ss Score
7.62
3' ss Seq
TGATGGTTTTTATCTTTTAGATT
3' ss Score
10.25
Exon sequences
Seq C1 exon
TTCCGCTATGGGGGTGACGGCTCCAAAGGACCAACCATCTCTGCGCAGGAAGCCCAGGCTCAGGCGATTCTTCAGCAGGCTCGG
Seq A exon
GTGAGAAACCATGAAGCCCCATTCACGTGACCTGATTCTGCATCGAACACCAGTGTGCAGGCCCACGGAAGAGTGGTTCTATGCACCACATGGAATTTGTGGAAAAAATCTGAAAAGCATATTTATCTTTCTAGGAATAATAGTTACTAACTTAATATTAAATAAATGACCCTTGTATTGCCACATGCAATGCTGACATTAGCCACCATGGTGTACAAAGCTCCTACTTTTAACAGGATATTGAGAGATTATATATAGTATTCCTTCCCTTCCACATCCTGACTTTTCTCTGCTAACTTGCAAGCCTATAATTATGTAAATAAATGTGAAAACACACAATGAAAGGAATATATCCCTCTAATTCACAAACCACATAAATAATTTCATTTTTAGTCAGCTTTAGAGCATTAAGATGTAATATTAAAATCCAGTCAACAAACAAGGAACGAGTCAGATTTCATATAATGCTTTTGTTCATAATTTTATAGTCATCAAGGAAGAAAGTAAATAGGACTTAGGATTAGTGTCATTATGATAACTGTATTTGTATCATGTCTAAGATAAATTTTAATTATAATCATAATTTATATATACATTTAAAATAGTGAATATGGAAATGAATTTATTAATTCATTTTCAATATCAATTAATAATAAAACAATTATTCATCTGAAAAGCGATTATTTGATTGAATGATAATGAGAATATTATTATATTATAATATTAGAATATTAGAATAATATTATATTATTATTAAATTACTTAAAATAACTAATTATCTACATTTTTAAGAAATTTTATTGTTTTGAATAAGTTAAAATTAAAAGTTTTTCAGGCTAGTTAATTTCTTGTTTGATTAGTCCTCTTTTTATTCTTTACTGATCAAGCATTTCCCTAAAGCATATTATTTTTTTTTCCGGAGCTGGGGACTGAACCCAGGGCCTTGCGCTTGCTAGGCAAGTGCTCTACCACTGAGCTAAATCCCCAACCCTCCTAAAGCATATTATTAATGTCTTTTGATCAAGTCATCCCCCAATTCCCTCCCTTCAAATTCTTCAGCTAGCTCCACTTCCATTTTCTCTTGATTTTCATGTTTTTCTTTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTCATTTACTTATTTATTAAACCTGCTGTGTTCATTTATTCTGCTTGTACACTCATGGGTATAGTGTTGTGTTTTATAAAAGGAAAAGAAAGTCAGTTTGATGGATATGGTGTATGTGTGTGGGATGCCTCTGTGGGCCCATGCTGAGGCGTCCTTTATTCCTTAGGTACCAGTCATGGAATGTATAGTTTAGAATAGAGTTCATTTAGGACCTGGGAAGGGGAGTTGGGAAGGGAGTACAGACACAGACAGGCAGACAGAAAGGAAGAGGAGGGGGAGGAGAAGGAGGGGGGAAAGAAATAGAAGCTGTGAGCACATGGAGAGGCTGGAGGGGAAATGGGGAGAGCAGGGACAGAGAGGTCAGAGAGTAAGAGGGTAAGAGAGTAAGACATTAAGAGAGTAAGAGTAAGCGAGTGAATTGAGAGCTCTCAGTTCCTTTTACAGTAAGCTGGGCATTACCCGGCTGTTACCAGGTAACTGGGGTGGAGTCTAGAAGGAATGATAGGACCATCTCCTTGAGCTGGGTCAGTCAGGTACGCCATTTCCTGACAAAACTTGACAGTGGGAGTTCCTGATCTCCTTTCTGCTCCGTGCTCTGGCTGTGTGTGGCTGGATCTTGTGCAGGTTGTGGGCACACTGTTCGTAGCATCTCCTGGTTCTTATGTGCGTCTGTCCAGCTGCATCCGGAAAGCACTGTCTCATCATAGTCCTCCATCTTTCTCACTCTTACATCAAGTTGGGAGGTTCCGTGTTCGTCACCTTCTACTGCTGAAAGAAGCTTGTAAAAAGAGGGCTGAGAGAGTCCCTAATCTAGGGCATGATGATGTTTTCACAGTCAGTTAATGTGACTTGTCATCTTAACTTGTTTAGAAAACAGATAGCGAGATGTTGAATTCCAGATATCTAGCTTATTCTTACTAATTTAGAAGTGAGTTATTGGTGGACCTTCAGAGATCTTCCTGATTTTGTTTCATGTGTTATATTTTTTATGATTTTCAGTCATAGGGTTATTTTTGAAATACACATTCATCTTTCACTCGTTAATATTTAAAACAGTAGATCTAAGTAACTTAACATCTATCAAGGACTTTTTCTCTGCTCTGCACTCTGGTTTTTCAAATACCCTAATTTCATATTTTTTTTGTCATGGAGTCTAATGATAAAGCACCCGATCAGTCTATTTTGTCCACAGAAAGAATTCTGAATTGTACTGCTACACGCTAATCACCGTAATTTATCTTAAAACTCTACTAGAAAACATTTACCTTTAATTGTTCACCTTTATTAAAGATCTCCAACCAAGATCTTCACATGCCTGCACAGTGAAGACAAAGAAGGCTCTATCTTTTGGAGTGTGCTTCATAGTAGAAAACTATTAGATAATCTATTTTTTTCTGAAATCTATTTTTAACTGACTAAATTTTGGCAGTATATTATTCAAGACTCTATAAGTTTGAGACATGAATAGTCATTAAATAGAACGTTCTAGTTACATGTACTTCACCACTGACTAAACTTTACTAGCATGTTGCTGGTATACCTTTGTTAGTTTATATACTACCCAAGGACATCCTGTCCAAATGACTTGTGCTACAACATACTACTAGGCAAGCCTTCCTAAACTTGATGGTTTTTATCTTTTAG
Seq C2 exon
ATTGCTCTGAGAGGCCCTCCTGGCCCAATGGGTCTTACCGGAAGACCAGGTCCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:13
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.4=84.2)
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]