RnoINT0038813 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216956747-216959043:+
Coord C1 exon
chr2:216956747-216956800
Coord A exon
chr2:216956801-216958998
Coord C2 exon
chr2:216958999-216959043
Length
2198 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TGTATGTTTGCTCCATATAGGGT
3' ss Score
7.22
Exon sequences
Seq C1 exon
GGACCACAAGGAAAACCAGGGCTTGCAGGACTTCCTGGTGCCGATGGACCTCCT
Seq A exon
GTAAGTCAAAGCTGTCTATGTTGTCACTGAGATTTCCACAAGCAATCATAGTAGCCTCTGTATAAAGTGACCCCATGCTGCACAGCAGAACCTGCCAAAATCTCTCCTTCATAATTCCACATGTTCCTTTATTTCAGTCAGCTTGTATTTTCAGTGGCTATTACTTTTTCATGCCTGCTTCTCCTCATAGAGAACATGAGTTCATCCACTTTTTAACTTGCCTCTTAGTCTTCAGCCTTAGGATGTCAGTTAATAAAACCCCATGGCCAACAACAACCTGGGGGGGATAGGGCTTGTTTAGTTCCATATTATCATCCATCACTGAGAAGTCTGGACAGGAAATCAAGCAGGGTCGGAACATAGGAAGGAATTTACACAGAGACTGTGGAGGAGTGCTGAGTTGGTCTTGTCTCTCTTGGCTTGCTCAGGGTGCTTCCTTGTAACCCCCAGCACCACTTGTCCCACCTGAGTACCATACAAAATGGGCTTGGTTCTCCCAATCACCAACAAGAAGATGCTTCTAGGCCAGTCTGGTTGGGCCATTTCCCCAACTGAGATTCCTGTCTTATCAAATGACTCTAACTTCTGTAAGTGAACATAGACAGACAGCACAAACACCAGGTGAAATCACACGGCAGGCATTGCTTTTTTCCTATTCTGTCCATGAAAAATTTTCAGACTATAGGGGCATTCTTCCTCCTGTGGGAATATAGAAATATCTGTTATTACTCTTTTTCACAGATACATATAATTTCTGCCTTTATTTTAAAATTATTTCTTATGTTGACTCTTCAAACTACTTAGTCTAGTCTCAAGCAAGATACCAGATTTCTTATTCTGTTTTTACCTGTGGATATAAAACATACTTTTGATTTTTTAAATATATAATATACATATATTTTATATATATATAAAATGACATCTCAATAGCATGATAATATGATTAGTATCTTTAGTTTTTCTCTGTATTTTCATCACATGCTCCTACTGACTTTTGAGGACGCTTTTGTTTGCATAAAGAGTATCAACCAAATGAAATTTGCTTCGTGTAAGATTTTGAGATTGAACTGTTAATAACAGGATGTATTATTTTATGTCCTTTCTCTTTAAAAAGATTTCATATTCAATGAAACAGACACTCATCAAATGTAATGTTTTTCTTCAACTACTAGCTTTCAATGTCATTAAAAGCCATGACCTTTGTACAATATTTTAATAATATTTTAGAATAAAGCATATGATTTTGGGGGTTCAAGAATCACCTCACAAACCATTTGAATACTTATCTTAGTCAGAAAGGGATAGTTTATTGGGCATATGCCCTAGGACCTGTTGAACAGGTTGACAGGTCTAGATTCAGGAGTTGAACCATAACATTGAGTTAATTTCCTACAGAGTTTTAAAACCAAAATCTACAAATATCTGTGTGAAGTTATTTCCCCAGTCAGGATTTAGGCATAGGAGGTTTCCCTTGGAGCACGTCTTTGTTGTACAATTATTCTGCTCCCCTTGTTTGTGGCATTCAACTGCAGGGACGACCTGCCTTGTCTAATATTCATGCTCCAATTTGTCTACTAGGATGGGACTTGACCCACACTCATATCTTAACTTATCAACCAGGATGTCAGTTACCCAATAAATGTCTCTTTTTGCCAAATAAGATGTCAGTTCCCAGGGAGGTCTTGGGAAATGAAACTTTACTACACCACTACTCAAAATGGAAGTCTTATTCAAACTGGTTTCCTATATTGGTCCAGGTGTCTCTTTTTTTGTTGGGGTGCATCACAGAGGCACCTGATATCATAAAAGCTTATGCATGGGTGCAGTGAGAATTGTTGGATGGTTGGTTTAGGTACAAGCCTATTGTGGGTAACTATGCAGTATAATCCGATTGACTTCTATCATGATTGGCTCCCAAAGGCACAGATCATAATAGAATATGTAATCTGTCTTGGCATTAGAAATTTTCCTAGTAACACCAGAAACATATGAGAAAGTTTTCTTTTAATGACAGAATATTCAGGTAACAATGATCTAGGCCTTAACATTTTATCTAGGCCATAACATTTCACTTAGGCCTTAACATTCCATCTAGGACGTAAGAATGATCTGATGTTTTTAAAGGAGTGGTAGGTATACCAAAGTTCACAGTTACCATAAATATCTTGTCTTTACCAGTGTATGTTTGCTCCATATAG
Seq C2 exon
GGTCATCCTGGGAAAGAAGGCCAGTCTGGAGAAAAGGGTGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:25
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(21.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.3=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:
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]