RnoINT0038850 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:217040140-217042458:+
Coord C1 exon
chr2:217040140-217040247
Coord A exon
chr2:217040248-217042404
Coord C2 exon
chr2:217042405-217042458
Length
2157 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
GATACTCTTCCCCCCTATAGGGC
3' ss Score
9.73
Exon sequences
Seq C1 exon
GGACATCCTGGTTTAATTGGATTGATTGGCCCTCCAGGAGAACAAGGGGAAAAGGGTGACAGAGGACTTCCTGGGACTCAAGGTTCTCCAGGAGCCAAAGGTGATGGG
Seq A exon
GTGAGTATAGTCAGATGGTTTGGCCATGTCGTTACGACAGCACAGTATAGTTACACATTCACACAGGATTTTATGATGATCACTGGAGGGCTTTAGGGCACCCATATTCTTACCTGCTTTAGTTTATGCTCCTTTAAAAATAGATAGAGGCCTTATTTCCAAAATATACAAAGAACTCAAGAAGTTAGACCGCAGGGAAACAAATAACCCTATTAAAAAATGGGGTTCAGAGCTAAACAAAGAATTCACAGCTGAGGAATGCCGAATGGCTGAGAAACACCTAAAGAAATGTTCAACATCTTTAGTCATAAGGGAAATGCAAATCAAAACAACCCTGAGATTTCACCTCACACCAGTGCGATTGGCTAAGATCAAAAACTCAGGTGACAGCAGATGCTGGCGAGGATGTGGAGAAAGAGGAACACTCCTCCATTGTTGGTGGGATTGCAGACTGGTAAAACCATTCTGGAAATCAGTCTGGAGGTTCCTCAGAAAATTGGACATTGAACTGCCTGATGATCCAGCTATACCTCTCTTGGGCATATACCCAAAAGATGCCTCAACATATAAAAGAGACACGTGCTCCACTATGTTCATCGCAGCCTTATTTATAATAGCCAGAAGCTGGAAAGAACCCAGATGCCCTTCAACAGAGGAATGGATACAGAAAATGTGGTACATCTACACAATGGAATATTACTCAGCTATCAAAAACAACGAGTTTATGAAATTCGTAGGCAAATGGTTGGAACTGGAAAATATCATCCTGAGTGAGCTAACCCAATCACAGAAAGACATACATGGTATGCACTCATTGATAAGTGGCTATTAGCCCAAATGCTTGAATTACCCTAGATCCCTAGAACAAACGAAACTCAAGACGGATGATCAAAATGTGAATGCTTCACTCCTTCTTTAAATGAGGAAAAAGAATACCCTTGGCAGGGAAGGGAGAGGCAAAGATTAAAACAGAGACTGAAGGAACACCCATTCAGAGCCTGCCCCACATGTGGCCCATACATATACAGCCACCCAATTAGACAAGATGGATGAAGCAAAGAAGTGCAGACCGACAGGAGCCGGATGTAGATCGCTCCTGAGAGACACAGCCAGAATACAGCAAATATAGAGGCGAATGCCAGCAGCAAACCACTGAACTGAGAATAGGTCCCCTATTGAAGGAATCAGAGAAAGAACTGGAAGAGCTTGAAGGGGCTCGAGACCCCAAAAGTACAACAATGCCAAGCAACCAGAGCTTCCAGGGACTAAGCCACTACCTAAAGACTATACATGGACTGACCCTGGACTCTGACCCCATAGGTAGCAATGAATATCCTAGTAAGAGCACCAGTGGAAGGGGAAGCCCTGGGTCCTGCTAAGACTGAACCCCCAGTGAACTAGTCTATGGGGAGAGGGCGGCAATGGGGGGGGGGTTGGGAGGGGAACACCCATAAGGAAGGGGAGGGGGGAGGGGGATGTTTGCCCGGAAACCGGGAAAGGGAATAACACTCGAAATGTATATAAGAAATACTCAAGTTAATAAAAAAAAAAAAAGTGAAACATCAAAAAAAAAAGATTAAAAAAAAATAAAATAAGAATGTGATACAGACAGTTATAAAATAGGGTATAGCATAGAAATAACTGAAAAATTTACGAGAAATGGAGTCCAGCTCAAATAGTTTCCAAAGAAAATACTTTGAAATTACTTCTTGGGGAGAGAAACATGTCCCAGTTAATTCAGGACTATTTTTAATTGGTTTGTTTTTCAAATTTTCTGCATATCACATACATTAAATTTTTAGTTAATAAAAAAAAAATAAAAATATTTTAATAAATTAAAAATATGATTTAAGTTAAAATAATAAAAGACACAATGATGTAGATGTTTGTACCACTTATTCTTGATTCTACATTATAATCCAGTCTTATTTTGAAAGCTTTAGAGATGCCATAATGAATGTCTGTATAGCCCTCATAGCAGTGACTTAAAGCTATATATTGCAACGAATGGAAAAAGTCTTGGATTACTGAACAATATTTCATAACAAAAAATTATTCACTGTCCATAAATTTTCAGATTTTTGCAATATATGTAGCAAACCATGAAAAGGAAATGAACTAATATCCTTACTAATTGGATACTCTTCCCCCCTATAG
Seq C2 exon
GGCATCCCAGGTCCTGCTGGTCCCATAGGTCCTCCTGGTCCTCCAGGATTACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:59
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=PD(7.9=16.7),PF0139113=Collagen=FE(45.5=100),PF0139113=Collagen=PU(7.9=13.9)
A:
NA
C2:
PF0139113=Collagen=PD(20.8=88.9),PF0139113=Collagen=FE(27.0=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]