RnoINT0038820 @ rn6
Intron Retention
Gene
ENSRNOG00000023148 | Col11a1
Description
collagen type XI alpha 1 chain [Source:RGD Symbol;Acc:2372]
Coordinates
chr2:216970398-216978821:+
Coord C1 exon
chr2:216970398-216970451
Coord A exon
chr2:216970452-216978767
Coord C2 exon
chr2:216978768-216978821
Length
8316 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GATTACTTTTCTTCTTTCAGGGA
3' ss Score
10.74
Exon sequences
Seq C1 exon
GGAAAACTTGGGGTTCCAGGATTGCCAGGATATCCAGGAAGACAAGGTCCAAAG
Seq A exon
GTAAAATAATTTGAAATTTATATGTCTATGTGATAAACAGTTAAATTAACAATCTAAACTTAGAAACTTATTTTTAGATCAGGAGAAAAGAAAGAATAAAATGCAGTTTTCTTCAATTTAATACTTATCACCAAATAAAAAAATAAACATCCATGTATAATAAAACACACACACACACACACACACACACACACACACACACACACACCCGGAGTGTGCTTGGAGAGTCTTGCTTATGTTATGTCTTGGAGAAACTCTGGACACAGGATTTTTATGAAAGAAAAATTTTTTCCTTTGACAGTTGGAATAAGAACATGTGAGGGAAGAACACTAAAATATTTTTAATTACACAGTAGATGTTATATGGAAAATACCATTTTATTTTATTTCTATTACCATTGTGGTTTGAGCCATTTAATTTTTATTTATTTATTTTTTGTGTATGTACATGTGTGCTCACATCCAAAGGCACATATATGAGGGACAGGGGACGGTTCTCAGGGATGAATTCTTTCTTTCCACTATGTGAGTTCCAGGCATCAAACTCTGGTTCTCAGGTGGAAAGTGCCCATAAACAGTGAGCCATATAGCTGGCTCTGTTCCATTATTTTTAAGATAATTGACTCTCCATTATACCAACATACATTTCCTAAGAGTGTTGTAACAAATCTTTGGTGAGTTAGAGCAAAAGAACATTTTACCATCGCCTTTCTTAATAGTAGAAGTCTGTGATTAAGGTTCTGTTGGGACCAAATACTCTCCAAAAACTCAAGGAGAGAATGTGTCCTGGTTTCTTGTAGCTTATGCTACGTACTGGTTTCTTGGGCTTGAGGATTCATCCTTCCAGGACTTTCTTTTCATACGTTCCTTTGGTTGATCCCTTCCCATATGTTTCTCCTGTAGACACTTACTTGTCTTTGGACTTAGGAAATGTTCATGTAATCTAGGATTTGTGGAAGATTCTTAATGTATCTTATCAGATGCTTTTCGGGCAATAAAAATGATGTTACAGCTTTCAAAAGTTTTTCCTTGTTTTTATCTGTTGGGGTACAATCAACTGTACTACTCAAATTTTAGTTTGTGATATTGAAATATTTATAAACCTTTTAACAATAAATAAATATAATTGTCTGCTTGTTTTGAAACATGGAATATTCTTCAGCTTATAAAAACTGTTACTGACTAGCCTTCATGTATTGACTAATTATTTTGATAGCTATAGAATTGATATGAAATCTTTAATTAATTTGGGGGTAGTTATTTCTTTTTTAAAGAGATGGTACCCTACTATACAGTCTATGGTGGCATAGAACTCCCAGTCCTCCTGATTCAGTCCCAGTATGCATGAATTAGAGGCATGTACCATCATACTTAGTTCATTCTTTAAGTATATGTACATGGGATGTATCGCTGTTCTAATATGTTTTCTTTACTTTTCTATTTTAATAGCTAAGCATAGCAAGTGTAGGAGGCACATGATAATATAATTCTAATTATACTACAACCTTAAGCATGTGTTAATAAACTTCATAGATAACTTGTAGGTGGCAAAACTTCCATCCACAACTGAAAGCCAGTTTTCACTCACCTTCAGACACAGTCTACATTAGGCTTTCCATGTGATTTGGTTATTATGTTTCCAAGAAGCCATTTATTTCTTATTCAAAAAGATGTATTTTTAAAGTGATGCGAGAGTCATTTAAATGTGTTTTAGTTTTAAAATGCTCATCACTTATTTTCCACCTTATTTGTAATATATTGCCCAGAATCCCATTTGCACTCTTTTCAAATATTAAGAATTCACAACGGTTATATCTGTAGAGAACCATTTGTTGCACAACCCAAATCCATAAACGTATTTTTATTTTATGTTGTGAATTCTTTATCTGTTCACTAAATGCATAGCAATCTTAATATTCATTCGCTTTGACTTAAAAATGATAGGAAACAGTCGTAATGTCATTTAAATGAGCACAGTTGTACCTTGCAGGTTTATATGAAATTATGTAATCCATTTTTTCCATTACGTATCAATTTTTTCATCAGTATTCTCTGAATTCTTACTATTAAGATATAAGAGCTGACAAAAGGAAAATGTTTTTTCTCACAATGAGATGGTGCTTTAACCTCAATGCCTAAACTTAGGCAGCTCAATTTCACACCACTTTTATTTTGCAGCGATAAGAATATTTCGCTTCTCATTAAAAAAAAAAACAAAAAACAAAAAACAAAAATGGGTTGGTCGCATTGGAGACCAAAGAGAACATTAAGCTTTTTTCCTATATGGAAGCCAGTGAAGATTTAATAGACGTTAGTGTTTCATAAAAATAAAAAAAACAAACAACTTTGGATGCTAAATTAAGGTCTTCAAGGCCTTTAGTTAAACACTGTCTGAGAAGCAAAGTAAGCTGGGAAGCCAAACCACCAAATGTAATAAAAGATGATAATTGTCTCAGAACCAAAAGCTTATTCTAAAGTAGAATATTTCTATAGTCAGTAGACCAAGTAGTTTTGCAAACTTTTTATTTATTGACAGAATGTTTCAGCATTAACTTGGGCCTGGTCTTTTATTTACTGTTTTTGATATTTTAAAGGTACTGTTTACTTGAATGTGTATTATGGACTTTGTTGATAACACCTTACATAAAAAAATGGAGGGCTTGAACATTTTCCTGGGTTTTCCCACATACTATGGAAAAATGATTTCAAGACATATATTAATATTAAGAAAAATTTTCATAGTGTATTTGTAAATAGGGTAGTTTCTTCTGATCAGAGCAGACATATTTGTTTACATATAAAATTTCAGTAGTGAATGTCATCTACATATCAGATCATACTTGCATGTTAAATTCTTAGTCACCCTGCAACTAAGAGTTATGGCTTCCAGTGCATTTGAAGAAAAAAATGGAAATGGAAGGTTTCAAACTTTAATAGTAATGTGCCAAGTATTTCTTACCATTTAGAACTTATATATTATTTGCTCTCAAGTAAATCAAAAGCACTTTTATAGGAAACACAAAATATACTGAAAATCAAATCATACAAACAGTAATTTGTACACTTTACATCATTATTTGACTCAGTATTGAGGTGAAACATCCCAATTTTCTTGACTCGCTTGTTTGCTAAACATGAAGCATTTGCCGTCTTCAAGTGGCAACAGAGCTCAGCACCTTCTTTATGGGTCTACAGGTGAATTTTCTCTTGTGCATTCAAACTTCTTGCTTCTAATTTTTCTCCATAATTCAGTGTGGGTCATCTGTAGAGGCCACTGAAATGATTCCTAAGCGTCAGCTTCAGGAAGTCTGGAATGCTACTTCCAATATTTAAAAGTATTACAGTCTATTCTAATTTATTTTTGCCTTTTACAACTTTGGAGACAATATTTTGGGGAGAAATCCAATGTAAAGAAGTTGATTTAAAAACACAAAAACAAAGAAATCAAAGAATATTGCTGTATGCCAAAGTACATGGAGATGTGTAAAAATTATAAAAATCTGCATTCTCTCAGCTAGTCATCTTACACAATATTAGATTTCATCCATACAATTGTTTATATAAGAAAGATAGATTTTTTTGCAACCCCTCCCCAATACACATACCATTTTAGGATAACATTTACAAAATGTTGGAAAGGGGTTAAAATTCAATCTTCTCTCTTTATTTATTTAATAAAGACCTAAAACTGCCTGGATAATGGTGGAAAAAAACTCTGAGAAAAGTTTGGGCATTTCCCAAACAAGAAATGGAGGAATTTTATTATTGGGATTAACCTATATTTCACTAGTAAAATACAGCCATTTATATTAAATGCTCTTATGGGCTTATTACATTTCTAAACAATCACTGTTCACTTTCTAATATTATCATTTTATATCTCACATACCTGCATTGATGAATGCTGAACTTCTTTTTTCATATCTCCCACAAACTTCAAAGTGTTAAGATGTCCTAATAGCTGGTTCCTTGATAAAATCAACAAGATAGATAAACCCTTAGCCAGAATAACCAGAGGACACAGAGAGTGTGTACAAATTAACAAAATCAGAATTGAAAAGGTAGACATAACAACAGAATAAGAGGAAATACAAAAACTCATCATCCTTTTGCAAAAGCCTATATTCAAAAAAACATGAATATCTGAAGGAAATGGAAAATTTCTAGACAAACACGAGGTACCGAAGTTAAATCAGGAACAGATAAACCATTTAAACAACCCCATAACTCCTACAGAAATAGAAGCAGTCATTAAAAGTCTCGCAAACAAAAAGAGCCCAGGTCCAGATGAGTTCAGAGTAGAATTCTATCAGACCTTCATAGAAGACCTCATACCAATACTATCTAAACTATTCCATAAAACTGAAACAGATGGAGAGCTACCAAATTCCTTCTATGAAGCCACAATTACTGTTATATCTAAATCACACAAAGACACAAAAAGGAAAGAGAACTTCAGACCAATTTCCCTTATGAATATTGACGCAAAGATACTCAACAAAATTCTTGCAAACAGAATCCAAGAGCACATCAAAACAATCATCCACCATGATCAAGTAGGCTTCATCCCAGGGATGCAGGGATAGTTTAATATACTGAAAACCATCAAAGTAATCTACTATATAAACAAACTGAAAGATAAAAAGCACATGATCATTTCATTAGATGCTGAGAAAACATTTGACAAAATTCAACACCCCTTCATGATAAAAGTCCTGGAAAGAAAAGGAATTCAAGGCCCATAACTAAACATAGTAAAAGCCATATATAGCAAACCAGTAGCTAACACTAAACTAAATGGAGAGAAACTTGAAGCAATCCCACTAAAATCAGGGACTAAACAAGGCTGCCCACTCTCTCCCTACTTATTCAGTATAGTTTTCAAAGTCCTAGCCAGAGCACTCAGAGAGCAAAAGGAGATCAAAGGGATACAGATTGGAAAGGAAGAATTCAAAATATCACTATTTGCAGATGTTGGGATTGTATATTTAAGTGACCCCAAAAGTTCCACCAAAGAACTACTAAACCTGGTAAACACCTTCAGCAAAGTGGCTGGGTATAAAATTAACTCAAATAAATCAGTGGCCTTCCTCTACACAATAGAGAAACAAGCTGAGAAAGAAATTAGGGAAATGACACGCTTCATAATAGTCCCAAATAATATAAAATACCTTGGTGTGACTTTAACCAAGCAAGTGAAAGATCTGTATGATAAGAACTTCAAGTCTCTGAAAAAAGAAATTGAAGATCTCAGAAGATGGAAAGATCTCCCATGCTCATGGACTGGCAGGATAATACAGTAAAAATGGCCATTTTACCAAAAGTGATCTACAGATTCAATTCAATCCCCATCCAAATACCAACCCAATTCTTCATAGAGTTAGACAGAAAAATTTGCAAATTCATCTGGAATAAGAAAAAACCCAAGATAGCTAAAACTATCCTCAACAATTAAACGACTTCCAGGGGGAATCACTATCCCTGAACTCAAGCAGTATTACAGAGAAATAGTGATAAAAACTCTATGGTATTGGTACAGAGACAGGCAGATAGAACATTGGATTAGAATTGAAGACCCAGAAATGAACAAACACACCTATGGTCACTTGATTTTTGACAAAGGAGTCAAAACCATCAAATGGAAAAAAAAGATAGCATTTTCAGCAAATGGTGCTGGTTCAACTGGAGGTCAGCATGTAGAAGATTGCAGATCCATCCATTCTTATCACCCTGTACAAAGCTTAAGTTCAAGTGGATTAAGGATCTCTATATCAAACCATATGCACTCAAACTAATAGAAGAAAAAGTAGGGAAGAATCTCAAACACATGGGCACTGGAGAAAATTTCCTGAACAAACCACCAATGGCTTATGCTTTAAGATCAAGAATCGACAAACGGGATCTCATAAAGCTACAAAGCTTCTGTAAGGCAAAGGATACTGTCGTTAGGACAAAATGGCAACCAACAGATTGGGAAAAGATCTTTACCAATCCTACAACTGATAGAGGGCTTATATACAAAATATACAAAGAACTCACGAAGTTAGGCTCCAGAGAGCCAAATAACCCTACTAAAAAATGGGGTACAGAAGTAAACAAAGAATTCACAGCTGAGGAATATTGAATGAATGAGAAGCACCTAAAGAAATGTTAAACATCTTTATTTATAAGGGAAATGCAGATCAAAACAACCCTGAGACTCCACCTCACACCAGTCAGAATGGCTAAGATCAGAAACTCCGATGACATCAGATGCTGGAGAGGATGTGGAGAAAAAGGAACACTCCTCCATTGTTGGTGGGATTGCAGACTGGTACAACCATTCGGGAAATCAGTCTGGAAGTTCCTCAGAAAATTGAACATTGGACAACCTGAGGACCCAGCTATACCTTTCTTGGGCATATACCCAAAAGATGCCCCACATATAACAAAGACACGTGCTCCACTATGCTCAGAAGCTGGAGAGAACCCAGATGCCCTTCAACAGAGGAATGGATACAGAAAATGTGGTACATCTACACAATGGAATATTACTCAGCTATCAAAAACAATGACTTTATGAAATTCATAGGCAAATGGTTGGAACTGGAAAATATCATTCTGAGTGAGGTAACCCAATCACAGAAAAACACACATGGTATGCACTCATTGATAAGTGGATATTATCCCAAATGCTTGAATTACTCTAGATGCACAGAACACATGAAACTCAAGAGTGATGACGAAAATGTGGATGCTTCACTCCTTTAAAAGGGGAACAAGAATACCCTTAGGAGGGGATAGGGAGGCAAAGTTTAGATCAGAGACTGAAGGAACACCCATTCAGAGCCTGCCCCACATGAGGCCCATACATATACAGCCACCAAGCTAGATAAGATGGATGAAACAAAGAAGTGAAGGTTGACAGGAACCGGAAGTTTAACTCTCCTGAGAGACACTGCCAGAATATGGCAAAAACATAGGTGAATGCCAGCAGCAAACCACTGAACTGAGAATGGAACCTCCATTGAAGGAATCAGAGAAAGGACTGAAAGAGCGGAAGGGGCTTAAGACCGGATATGAACAACAATGCGAACCAACCAGAGCTTCCAGGGACTAAGCCACTACCCATGGACTGACCCTGGGTTCCAAATTCATAGGTAGTAATGAATAGCCTAGTAGGGGCACCATTGGAAGGGGAACCCCTTGGCCCTGCCAAGGCTGTACCCTCAGTGAACGGGATTGTTGGTGGGAGGGCGGTAATGGGGAGAGTATGAGGAGGGGAACACCCATATAGAAGGGGAGGGGAAGGGTTAGGGGAATGTTGGCCTGGAAACCGGGAAAGGGAATAACATTTGAAATGTAAATAAATACCCAATTTAATAAAGATAAAAAAATATAACGTTATTATGTTTGACTTTAAACACTTACTTAAATGGTTCTTCAATGCTGTATTTGACTGGTCATACCTGACAGACATAATCCATGACTGTGAGGTATTTATAATTTAGGAGTAAATTGATGATGGTATATTGTTTACAAGGATATTACAATTCCCAGTGTTATTTTTCCTCTTTGAATTTGTTTCCCATTTTCCAGAATTATGAACACTTAAAAAAAAAGTCCTAATAGATCTTTGCTCTCCCTGTAACAATAAATAGATCAGAGTAGGAGACATTCCCTTTCATTCTTGGATGCTGTTGGGAAGCATAAGATATGAATTAGGTTCTTTGGATTTCCAAACATAGATTTATTTCTTACTTATGTTACCAAACGAATGTGATAATATTCAAAACCAGTTAGAAAATGTAAATAAAGCTTTTCATCTCCCATAATATAAAACAGCTTTAAATCAAATATGTGTCTATTAAAGAGGTACTTGTACAAATGTATTAGCATTAATTAAGGACATACTTAAGCTGTTACTGTACTTTACGAAAATATGATTTTCTTTTAGAATTTGAGAAAATGTATGAAATATTAAATTGAAATATATTTTCATAAAATATCCTTCACCTTCTATTTGAGAATAAAAATGTAACTTAATCCTTTGGTTTTAAATTTAATACTAAAATATTTTTTATCAATTCATGCCTGCAGGCTTTCAGATGTCACTGTAAGTTCGCTTTCGAATTCAAGAAGGCACCTTGTGTAGTGATCAAAATGCATTTGTTTTTAAATGTCATATTTTTTTATCATACACTTCCAAAGCAAGAACATGCTTCTTACTTGAATACTACCATCTAAGACCAAATCCATGCTTACTAAAATTAATGCAACTTGTGACACGAAGAAGGAAATTATCATATTCATTGATGATTACTTTTCTTCTTTCAG
Seq C2 exon
GGATCCACTGGATTTCCTGGATTTCCAGGTGCCAACGGGGAGAAAGGTGCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023148:ENSRNOT00000068413:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.944 A=NA C2=0.541
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.9=100)
A:
NA
C2:
NO
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]