RnoINT0040041 @ rn6
Intron Retention
Gene
ENSRNOG00000003736 | Col5a2
Description
collagen type V alpha 2 chain [Source:RGD Symbol;Acc:70921]
Coordinates
chr9:52109212-52110558:-
Coord C1 exon
chr9:52110505-52110558
Coord A exon
chr9:52109266-52110504
Coord C2 exon
chr9:52109212-52109265
Length
1239 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TACGTTTTGTTAATTTACAGGGT
3' ss Score
8.71
Exon sequences
Seq C1 exon
GGTGGCGTAGGAGAGAAAGGTGCTGAAGGAACAGCTGGAAATGATGGGGCAAGG
Seq A exon
GTAAGAGACATGGGAAGGGCCTTTTCCACCATGGGCTACAAACCTACATTTCTGCTCATTACCCTACAAACTTCCTGTAAGTTTTAGCAACAAATTAATCATGATGTTTTATAGTCAAGAGAATGATGCAATTTGAGACTGGATGTAGATTGATAGTGCCTACTTATTTTACTTACCCTGCATTAGTGAAATAGAAAAATGCAAAGTCCTTCCTGAAAGAATAAAAGGAAACAAACAACTATCCCTATATCTCTGGCACTTAGGAAAATATGTGTGATAGATCAGGCTAAATACAATCATTGTCTATTTGTAGTAAGTGCAATACATTGTTTTAGGAAACAGTCATTTCTATAAGGAAAAAATAATGTCTTCTTTGTTTTAAGAACACCTCCCCTGTAGTAATAGGGAACTTACTTTTTGTATCCATATAAGCAACAAAGTGATTTTATACAGTTTTAGAAAAAATATTAGAAAAATATATAATATGTTTTCCATATTATATCTGGAGAAAAGAATGTTTTTCTCAAGAACATACAATTAATAAATCAATATTATTCTTTACATTCTTATATATATGTATATATATATATGTATATATGTATATATGGAGAGAGATAAAATATTGAGGGGCCTATGAGGAAGAAACATAAAATTAACAGAGAACTTGTACAGAACTCCCAAAAATTTATTTAATTATTGTGATTATGTGTTGTGAGCCTCCAAGTCCTGCCCCATGTGGTGGCCCCATTCTCCCTGTGTAGAGAACAGCACCAACAGCAATGAACCTTGACTGTGGATGGCTATTTTATCAACAATGAAGACATTTTACTGTAACTGTATTTTAAATAAAAGAATTACACTTTTTTATCATATTAAAATTAAATATATTACAAAAGAAAATTCAATTTTCAATCTCTTCTCAACATTCAAAATAGATACTAACAAAATTAAATGGGTTACATTAACAAAATGCTGCTAATTTAGAACTTACTTGAAGACAGTTTCTTATACTGAGCAGAGTTAGATGAAAGAAGTCAAAATGTTTTTTAGAGAAAAATCTCATTGCTAGATTATGGATGACATAGCAAATTCCCAAAAGTGGTGTCATCTATAGTAGATAATGACTTGCAAAAGCAATCATGCTACAACAAAATAGCTGGTTTGTTTGTCTATTTAATTAAACACGAAAACTTCTGTACACTCTTTTCCTCGGTATACTTACGTTTTGTTAATTTACAG
Seq C2 exon
GGTCTTCCTGGTTCCTTGGGACCTCCAGGTCCTGCAGGCCCTACTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003736:ENSRNOT00000005073:36
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=FE(24.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(24.3=100),PF0139113=Collagen=PU(3.1=11.1)
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]