RnoINT0038857 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217050925-217052999:+
Coord C1 exon
chr2:217050925-217050993
Coord A exon
chr2:217050994-217052765
Coord C2 exon
chr2:217052766-217052999
Length
1772 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
TCATTACTCTTTTCTGCCAGCTT
3' ss Score
6.81
Exon sequences
Seq C1 exon
GTAAGACTTTCATCTTGGCCGAAGGAGAAACCAGGAAGTTGGTACAGTGAATTTAAGAGAGGAAAACTG
Seq A exon
GTATGTTGCTGCCTCCATATCCAACAAAATCTCTTAAACTCCTTAGGTGAAGCTCCAACCAAGTGTCCTCAGAAGCTGAATCAAATACATAAGTAATGCCATGAAGAGTTTCGCATGCTTCCATAGTTCCCAGCCTTCAGGTCTTAGACATCAGTAATACCTTAAAGCTTAAAGCATTGAATCAAAGTAACTGAAAGGATTTATGAAAAAGAAAGTATAATCAAATGAAAGATGCGGCTTAGCATCATAAAACAGGGTTTTTTTTTTTAATAAAAGTAGCGAGAGTCAAAATACATCATCTACCTAGTATCTCTAACTCCATCTATTTTAATTTCTGTCTCCTTGAAACACAATTGCTCTTTGTTCCTAATTCAACGAGAACCTGAAGAATGTGCAAGTTTTCCCTCCTCGGTTTCATGAATATAATAAACAATTGACAGCTGAATATAATAAACAATTGACAGCTCGTTTTTTGTGTGAAGCCCATTTTACTTAAATATTTCAATGCAGTGACCAATTCCATGTAATAGTTTGCTAGAAATAAAGTAAGATTAAAGCCCTAATTAAATTATATTAAAGGCTGTTAAAATGATTTTTTTAGCTAATTAGGAATTTCTCACTATTTCCCAATAATCCTGGTAATTATTCACTTATTTAATATTTTAAGTGGCATTACTTTCCACAACTAATAAATTATATATTTAATCCCCTTACTTATACACACGCATCGATATTCAGCAATGACTTCTAATGAAGCTTTCCACCTGACTTAAATATTTTTAGTCATATACTGGATATATGTGATGCTTTTTCATCTATTTCAGTGGTAGTAAACATATATAGAAGTGTAGGTTAATTTTATTTTAATTTATTTTACTTTGTGTAATGCACATCTAAAATACATTTCAACCTCACAAAAATCATCATTGCAATTTGTTAATTAGTAAGATTAAGTAAACTCCATTAAAAATAATACAGAGATTACAGATTTTCATGAACTCAATCTGAATACTTTATTTAAATCATGTACTACATACTTTCTGGAACACAGATTACTCCATTCCTGTCAAAATAGTTGAAGATGCCTATACCTTAATAATTTGCAACTCAGAACACTTTACTCTGTAAGAACAAGATCGTGATTGATACATACGTTGACTAAAGTTTTCTGGGGTGCTATGCTTGATGATGTTGATTTAAAAATAGAACCTATGCTTTACCTGAAAATGGACAAATTCCCATCTATGCTAAGAAGTCAAAACATTGTAGAAGACTAGGACAGTGTTAAAAATTCATGTAAAGTAGATAGATTGCAAGATTTCTGAAGAATCAAACCATATAAAAACCATCCACTGTTTACTTTGTGGCCACACTCTTCTTTTTTTTTCAAGAAAATAATTACTATCTTACCATTTAAAAATTTACAACTATACTTAAATATCTCTTGGAAGCAGAACATTTGCTCTCTTACAGTATTTACTTGTTAGAAAAAAGGCAGGAAGATAAAGTAAAGTAGTTTAAAATCTGAGCAGTATTTTAATAACTGAGGTGTGTGGGGAGTCCCAGTGCTGGGGGCAAAGCCCCTATCTGACTTTTTTGACTCTTGCCACATTTCTTTATAAAATGATAGTATTCCCTTTAGGATCACCAAGACCTGGCAGTGTTATTCACAGCCAGTATTTAACTATCCCAAGAATGAAGAACTGTAAAAAAATAAGAGTAATTGAAAAGGAAGAACAGTCCTGATATGCCTCATTACTCTTTTCTGCCAG
Seq C2 exon
CTTTCCTATTTAGATGTGGAAGGCAATTCCATCAATATGGTACAAATGACATTCCTGAAACTCCTGACTGCCTCTGCCAGACAAAACTTCACCTACAATTGCCACCAGTCAACTGCTTGGTATGACGTCTTATCAGGAAGTTATGACAAAGCACTTCGGTTTCTGGGATCTAATGATGAGGAAATGTCCTACGAGAACAACCCACACATCAAAGCTTTGTATGACGGCTGTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141013=COLFI=FE(10.4=100)
A:
NA
C2:
PF0141013=COLFI=FE(36.3=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:
GTAAGACTTTCATCTTGGCCGA
R:
GCACAGCCGTCATACAAAGCT
Band lengths:
302-2074
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]