RnoINT0038942 @ rn6
Intron Retention
Gene
ENSRNOG00000058470 | Col12a1
Description
collagen type XII alpha 1 chain [Source:RGD Symbol;Acc:2374]
Coordinates
chr8:87143247-87145235:-
Coord C1 exon
chr8:87145176-87145235
Coord A exon
chr8:87143511-87145175
Coord C2 exon
chr8:87143247-87143510
Length
1665 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATATGTCCAATATATTTCAGAGT
3' ss Score
7.37
Exon sequences
Seq C1 exon
TTGAAACAGGTGATCCAGCAAAACCAGGGGAGAAGAAACCTGGAAAAACAGAGATACAAA
Seq A exon
GTGAGTTTGTAGAAGTTACTCGTGCACTGTAGTAGGTGTTCTAATTATAGACAAAGCTTGCTCGTCTTCCCTCTATTAACGGCTATAGGCTTTCTCTGGAAGGAGTAAAAATGACAGAGAGAAATGTATAACTAAATACTTATAAGCCTTAAGTTATAACCTTCAGCCAATATTTCCCCCTACTACACATTGATAGCAATAGATGGTACTTACAGATATATGGGAAAAGACTGAGGGGGTCTTAGTGCGTGAAGCAACCCAAGTGCTATGGAATACACTTTGTCTACTTGCATACTGAGCTCATCTCTGCGACATTTCCATTACCTTGGCTGATGACGCCAGCTCTCCCGATCTTCCCAGAGTTTGCTGCAGCCCATCTCTAAGGACTTGGTGAACACATAACCAGATGAAAAGCACTTTTATTTAGTTTCAGCTGTGAGGCTCTTCGCCTCCTTTGTCTGATACTGCTTTGTGTGGCTTGCTAGAGTGAACTCCCAAGGAGTTTCTTGGACTTCTGATTTTGCCACTTTGTAAGTTGGATTTATGACCCAGACTGGCCATAAAAACATTGTAAGTACAAAGGCTTCTTTCTCTGGAGAATTTCCCTCTAGACCACTGTTTGTCATTCCCTCAGATGTCCAATAATCTAAAACGAAGTTTCTCTTATGCAGTTACATTAATATTTTCTCCAAACTATCAATATTTATTCTAAGTCAAAATATTCCACCAGATATGGGTTTTTAATAGACTAAAATTGCCCTATTAAACAGCATATAATTGTCTTGCACAATTTTCCAGGACCTTTTTCTGCTCCTCTTTGCCAAATACTTTTTTATTATCTACCAACCAACTTCAAGGACAAAAACATCTTCAGAAGTCCACTAAATGTTGCCTTGCAAATTCAGATTTTTCATGAACACCAACTTGCCTGCTTGACCACGGAAGAAAGAGAGATAATGTGTGGCCATAAAAGTCCATGGCATTTTAATCCCTTAAGGATGCCATATGGACATTTGGGCTTTTGACTTAGCCGTATTTCCTCTTTTCGTTTAGTAATGGAGATTTCAGTTGTCAAATTTGAGTACATAGATAACAGAGACATAGATATTTTGGCTAGTTTGCATGACTGCGTGCATAGACTACCCCGACTATAAACTTAGACGTTTATATTGGAAGATATGGCAGACTATTAAAACATTTGCTCTTTTCAACTCAGACACATCTGCTTGAGGAGCACAGATTGTATTTATCTGTTGATAAACAAGGAGGCGGGGGGGGGGAGACTCTGTGGACATTTCTTTTGTGTGTCTCCTGGATGCTTTATGTAATCTTCATACAAAAGATATGGTTTAGGAAAGCAGGCTGCCACTGCATGTGCTCTGACTGAGGTATCCTGGGCAGCGTTTCACATGTCTAGTCATTTCTTTGCACAGAATACTGTACAGTACAATGTAAAGGCATCTAAATCCCATACGTGGGGCTTGACAAGTGCACTAAAATTACTTCAGTGTGCTTTTGAGACTGTATATTCTTTTAAGTGCGTAGACAGAAAATAGTGGGTCAAATATATTCTAATGAAGATAGAATTCATTTGCAATGCTAGGCTGTGTTTTTTTAAAAGGTGGACTGATTTAATCACTTGAAAATATGTCCAATATATTTCAG
Seq C2 exon
AGTGCTCTGTCAGCGCCTGGACCGACTTAGTGTTTCTTGTGGATGGCTCCTGGAGTGTGGGAAGAAATAATTTCAAGTACATTTTAGACTTCATTGTTGCTCTTGTGTCTGCCTTTGACATTGGGGAGGAGAAGACAAGGGTGGGAGTTGTTCAGTACAGCTCAGACACCAGGACTGAATTTAACTTAAATCAGTATTACCGAAGAGAAGACCTGCTTGCTGCAATTAAAAAAATACCATACAAAGGTGGCAACACAATGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000058470:ENSRNOT00000077071:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.714 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0009223=VWA=PU(46.2=89.9)
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:
ACAGGTGATCCAGCAAAACCA
R:
CTGTCATTGTGTTGCCACCTT
Band lengths:
319-1984
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]