RnoINT0040254 @ rn6
Intron Retention
Gene
ENSRNOG00000010663 | Col6a5
Description
collagen type VI alpha 5 chain [Source:RGD Symbol;Acc:1565804]
Coordinates
chr8:114531972-114534029:-
Coord C1 exon
chr8:114533343-114534029
Coord A exon
chr8:114532069-114533342
Coord C2 exon
chr8:114531972-114532068
Length
1274 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
GAATTCCACTCTGTTTCCAGGTG
3' ss Score
9.17
Exon sequences
Seq C1 exon
AACATGAAAATCATAGCAGAAGAGAACTGAGTCTTGCTCAAGAGCCTGGAGATGCTTCTCCTCAAGAATATTACATGGATGTGGCTTTCCTCATAGATGCTTCTCAACAAATAGGACATAATGCGTTTACAGAAGTGAGAGCTTTTATAACTTCAGTACTAGATTACTTTCACATCACCCCAGCTCCACTGACCTCTGTCTTAGGAGACAGAGTGGCTGTCCTGACCTATTCTCCTCCAGGCTATCTGCCAAACACGGAAGAATGCCCAGTCTACCTGGAATTCGATTTGGTCACTTACAACACTGTACACCAAATGAAGCGTCATCTCCAAGAGTCTCTTAAGCAACTCAATGGAGATGTTTTTCTTGGGCATGCCCTTCAGTGGACAATTGACAATGTCTTTGTAGGAACACCCAATCTGAGGAAAAACAAAGTTATCTTTATAGTAACTGCAGGGGAAACCAACCCGTTAGACAAAGAAGTTTTAAGGAATGCATCTCTGAGAGCCAAGTGCCAAGGCTACTCCATATTTGTATTTTCCTTCGGTCCTGTACACAATGACTTGGAGTTAGAAGAATTAGCAAGTCACCCCCTGGAGCATCACTTAGTCCGGCTTGGTCGGGTACACAAGCCAGATTTGGACTATATCATCAAGTTCATCAAGCCATTTGTTCATTCAATCAGAC
Seq A exon
GTAAGTCACTCAAGCTTCTCTCCTTTCTTGCTTTATTAATGTCTCTGTGTGCAGTCAATCAGCTCACTTAGTGCATCTCATTTTCGTGGCGAGTGGTAGGATGGGAACAGGAGGAAGTAGAGAATCACAGAGAAAAGCCTGTTCACATTGTTGGGTACTGCTCCTCAAATAGGTGAAAGATTTCCTTTAAGCCTGACTTCTGAACATTTGCTAAGAGTTTGTTTCTCTGACTGGCTACATCAGTTAATCTCCAGTATAGCTCTCAAAGGGAAGAGTTCAGATTCCTTTTCTATAAAGGAAAATCTAAGGTTTGGATACATTAAAAAACCTGCTCAAAAGCTCATAATTAATGCTGGTGAATTCTAGTCTCAACCTCACACATTCTGACCCCAGGATTATGTTCTTTTCTATTAAGCTGCACATTAGTTACTAAACCCTTAACAAAGTGTACTACTATAATAAATAAACCCCCTACCATGTCACTGCCCTCTACTTTCCCCTAGGACATCTGGTCTACCTTGTCATTATTAACCAGCTTCCATTCTGACTTGAATTTTTATTTATGATTTTATAGGTACAGATATTTTCTAGAGTCTCTCTTCTAGATCTAGTTTAAATGCAACTACATAGAAATCTGAAATGTGCCTTCCACTGTGGCACTCTGAGGGTAGCTGCTTCAGCTTCTGTCTTTGGCACTGGTATGGAATAGGCTGAGTTTTTAGAATTATCAGACAAGTCCTGGTCTGTGCTAGAAACCCAGGGACAAAGCAAAAAGCCATGCCGTGTGGTTATCTGCAGTGGCTGAGAGCTTGTTAGGGTCACCCAGGATTTTAGGGGTTCTGGTACACATGCAATCCCAGGACTCAGCTTAGAGCTAGGAATCATGGAATTCCAGCAATATATTTACTACTGAGTCAAAAACAATGCCTTCTTTCAACCCCAAGGTAGAAATAGGGAAGACAACTTCGATAGCCAACAGAACCTACTAGGAAAAGCCTTCATTTGTGGGGTGTGGGGATAAGGGGAGAAGAGATAAAAGGAGGAATTCAGATATGTCCTTGTGGGAACTTTTAATTCAATTATTGCTGTATCTCATTAACTTTGCAAGAACGAGGTCTTTCAATGCCAGCATGCCAACCTTTGCCAAGACCCTCCGAAGATTAATTTGTTTTTGAAGAGACTTCCATCCCCAGGAAAAGATGAGCTGACTTTTTGGGTGATAGGCATTATGTGGGAAAGTAAAAACTGGACTAAGAATTCCACTCTGTTTCCAG
Seq C2 exon
GTGCTATCAACAAATATCCTAGCAGAGACCTGCAAGCCAAGTGTGCTAATCTCACTTTCCCTGGCCTGGAGAATGCTGGCACAGAAGACAGTATATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000010663:ENSRNOT00000038160:38
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.074 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=WD(100=80.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTTCAGTGGACAATTGACA
R:
CACTTGGCTTGCAGGTCTCTG
Band lengths:
356-1630
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]