RnoINT0038959 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87040799-87044183:-
Coord C1 exon
chr8:87044013-87044183
Coord A exon
chr8:87041780-87044012
Coord C2 exon
chr8:87040799-87041779
Length
2233 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
TGTAATGTTGAATCGGACAGAGC
3' ss Score
1.49
Exon sequences
Seq C1 exon
GTCCACAAGGTGAATCCAGAACAGGTCCACCAGGGTCTACAGGTTCAAGAGGCCCTCCTGGTCCCCCTGGTCGTCCAGGAAACTCAGGTATCCGAGGACCCCCAGGTCCTCCTGGATATTGTGATTCATCCCAGTGTGCCAGCATTCCATACAACGGGCAAGGCTATCCAG
Seq A exon
GTATGTTGATGCCATTGTAAGGACCCCGGTTCCCCAGAAACAAAGAGCCCTAGGATTGAAGGAATGTGGAGCCAGGGATCTCGTGGAGATGCTAACATTTTCAGTTCTATATATTGAGTATGCAACAGTATCTGTCTTCTCAAGCACAAAACACTTTCCACCATTAGGATTTGAGTCACCATTTTCCCCTCCTCTACTTCTGGATTTACCAAACCACACCACTAACCTCTCTACAGCTCTCTTAGGAGTTAAACGAATGCTACCCATTCATGAGGTTTTCTTGTTTTTTTTTCTTTCCTTTCTTTTTTATTTATTTATTTTTTACCCAAAGGAACAGAGAGACCAAAAAAAAATGAAATAGTGTTATAGAATGCTGAAAAATATACATGAAAATTATTTCTGCAGTCCCATTTACATGTGAGAGCAAACAAAGTGCAGACCTGTGGAATAACTCACTGCCTTGCACCATGGATAGAACTGATGCCCATCGAATCCAGAGCCTAATATTTTTGGGGGGTTGTTAATGAAATTCTAGTGCTGCTCTGTTGGAGACTGCAGAAGCATCTTGTGCCTCACCTTGGGGGGATGTAAGGTTTGGGGAGGGGGGGTGAAGGTCTGGATAGAAAGACTCTCAAGTTGTGATCGCTGGTTACTTTTTCATTAGAGCGCCCTCATGCATCTTGCAAGTTTAAAAAATGATACTGCTGTTTGATATGGTTTGCTATTAGCAAGTAGTGCATGAGTAGTTGGATATATTAATATCTATATATCTATATATTTATGTGCATAACTATATGTGATCAAAAGTAATAATGAATCCAAATGCACACTTTCCTGTAATCCATTCATAAGATTATAATTTAATTCTTTGTAAAGCAAATTTAAATTATCCCTGCCTTAGGGCATATATGAACTGAAAATATATGGATATATAAATATACGTACTTTAACATTTACATAGATGGATGTGTATATGTATATATTTTTGCGTAGTAATTCAACTTTTAAAAACTATCATCTTTGACCTGTTTCAGGTTCCGGCTAACAAACTTTCTAAGTCTCCAGTGCTGCTTACAGTTTGAATACATGAGAATCCTGTTTCTGAGATGTTTGCGCACGTGCTTATTAGAAAATGAGTCTGTATGGAAATCTCACGGCAGATATGGTTAACGAACTGGGTCGGCATCACACAGGAGGGTGGAGACTCCATACTAACTTGAATGACGCAACGGGCAGTGGTGTCCGCCTGATGCTTTTCAGCAGTAATGTAGAAAACCATCTTTTAAAAAGTCCGAATGCAGCTGGGAGGAGCCCTGGCTGTGAAGGAGGTGCCCTAATAAGCTACTAACCAGCAGAGACACGCCATGTTAAGACAGACGATTAACCGGGTTGAAGAGAAAGACCCCGTGTAAATAATCAACTAATTGTGGCTTGTACATGATCTGTATGTGATCCCGTGTACTAAAATTTCGTTAACCACTCAACAACCCGCTTCTGCGCTAAAGCCTGCTGGCCGTTTGCTCTCTGCAGTAATAACGAACAGATCTGATCCTTTCTTGCTTGTTAGCAGTGTGTCTGAGTTCAGGGCATGTGACTTCTCAGCATTCTGGGTGTGTACTTTTATTTGGGTTTCTTACCTGCAATCTTTCAAACCAAAGTTTAAAAATCACCGTTCCTTCCGGTTTGGCTGTAGTCACAGGTGTTCCTCACCCACTCACTGGCTGTAACTCTGCTGGAGACATAGCCATAGGGGACACGGTGGACTGTAGAAAACCTGGTGACAGCTCCTTTCACCCCGAGATCAATCTCTAGGCCCAAATACTCTTCATGTCCTCAGCTCTCGAAGTCATTTGCTAACCCTGATGAGTTTGAAGTCATGAACAGTTATCTGGGGATTTGCCAAAAAAAGCCTACCTAGGTACTGTGTTTACAATTCTTTGGCCCAATTTCTGATCCTTCCCAGGTTTTGTGCAATGATTGTGTTTACTGCTGGATATTTGCGACACCCCCACCCCCACCCCCACCCTACCCCCACCGCTGGCGCTCCTTATTCGATCACCAAATTCACCCTGCACATGTGCACATGGAAATAATCGGATCGCTGTAATGCAATACATCTATTTGTGGTTGTGAGATTAAGACTGGAGTATCGTCACCTCCAGTGATGACTTAACTTTTGCTGTGCGTGTGTACCTTCCAAGTCATGCTATAACTGTAATGTTGAATCGGACAG
Seq C2 exon
AGCCTTATGTGCCCGAGGGCGGGGCCTACCTGCCTGACCGCGAGCCCTTCATCGTACCTGTGGAGCCTGAGAGGACGGCAGAATACGAGGATGACTACGGGGCAGATGAGCCTGAGCAGCAGCACCCTGACCACAGGCGTTGGCGGCGAGCCCTACGCCCAGGCCCTGGGCAATGAACCTGAGACCACGGGTTCACCGAGGTGGGAGGTGTTGGGATTCTCATTCACAGGTCAGACAGAGCAGCAGTGACGTTTTCTCAGCGTCGCTTCATCCACAAGTGCTCCTATCTGACTGTAGAGAATCTTGTTTCTGGAGGCAGCCTAGCTCGCAACAGTCTGTAGACATCTTTGCCTTTGCAGTACAAATGGTCACAACACAAGCTTTTCACAGAAGCTGCATGGAGAGAACACACCCAGGGTGCGCTGGGGCAGCCGAGCTTCTTGGTTGCCCTGCAAGCCCTGGAAACCAGAGCAGCTGTCTCTTCAGAAAGGGCCTTTATCTTAGAACTAATCTGCAGTTCAATTGCACCCCATTTCCAGTCATTCCGCTCCTAAAATCAAAAAGAAGGGGGAACAGCAGCTCACTGTAGCCGGTCACCTATCTTTTCTTCCTCCTCTTATGCTTTAGGGCATAGTCTTTTTAACAACCACAGACCTTAAGCCTCGTAGCCGAAGTTATTGTATCAACTGGATACTGTTCCATATTGCTTTCGACGTCTTTGTTGACACACTAACATTTATGCCAAATTGCAGATTATTCTGCCGAGATGGAATTGCATGTTTGTGTTGTATATTTAGAATGAACTTTTTTTTTTTTTTGCAGAACATGTTTCTTAGTTATCAAAGCAGTTGGAAATGTTTGCAAGACTATGAACATAGAGTCGCTGCTTTTATATTTTAACTGCAGATTGTGAATTTCACTGCCTTATATTATTTATTTCTGAAACAAAAGAGGCATTTTTCAATAAAACTACTGAAAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.684 A=NA C2=0.646
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
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]