RnoINT0040005 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6563244-6565410:+
Coord C1 exon
chr3:6563244-6563279
Coord A exon
chr3:6563280-6565356
Coord C2 exon
chr3:6565357-6565410
Length
2077 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
CTTTGTTACTTTCTTTCTAGGGT
3' ss Score
10.63
Exon sequences
Seq C1 exon
GGCCCTCCAGGTCCCAAAGGTGCTAAAGGTTCATCG
Seq A exon
GTAAGTAACTGCCTTGACGGTCCATGACACCTCAGACTGCCCTGTAGGTAGGAGAGGAGTCCCCTTGGACTGGACCCCCAACCTTGGACCCCTACCCCTAACTACCCTGGACTCTCACCCTGGACTTCCACCCAGACTCTCACCTGGACCCCCATCCTAAACCTCTACCCTAGACCCTCACCCTGGACCCCCATCCTAAACCTCTACCCTAGACCCTCACCCTGGACCCCCATCCTAAACCTCTACCCTAGACCCTCACCCTGGACCCCCATCCTAAACCTCTACCCTAGACCCTCACCCTGGACCCTCACCCTGAACCCCCACCCTGGGCCCTCAATGTGGATCCCCACCCTGGAACCCCATTCTGGAACCTCACCCTGGACCCTCACCCCAGATCCCCATCCTGGACCCTCACCCTGGAACCCCACGCTGGTACCCCACCCTGGACTCCCACCCTAGACCCCCCACTCTAACCCATAGCTGTCCTCTCCACACCTCCTCTTTTCTTCCTCATGGCACCGTGTGCTGCTGCCATTTCTTGCTGTCTATAGGTTTTTGGTTTGAGGGGTTTTGTTTTGTTTATTTGTTGTTTTTTTTAAAATAACTATTCGATTGCTCTGCTGCTGGCTATTTTTTTTTCCTTTTTCTTTTTTTTGGAGCTGGGGACCGATGCTGCTGGCTATTTTTAAGTATTATTTTAATTGTAGCTGTTCGTGGAGTAAGGCAGGTGAAAACCAAGCAAGACTAGCTAGCTCTGCCAGATCCTGCAGCCTCTTGACACTTTTGTCTAACATGTAATAATCACATGTATTTATGGCCCTTTGTGTGGCTTTTTACTGTGTATACATGACATGTCCTGATCAAATTGGGGCCATTGGCATTCCGTGTCTTTATTGTTACTATGTGTATGGAGCCCTCCAGCCTCTCTAGATATTCATGCAACCTAGCAGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAGAGAGAGAGTATGTGTGTGTGAGTGTGAGTGTATGTGAGTGTCTGAGTGTGAGTGTGTGAGTGTGTGTGTATATATGTGAGTGTGTGTGTATATATATGAGTGTGTGTGTTTGTGTGTATGTGTATGAATGTGAGTGTGTGTGAATGTGTGTGTGTTTGTGAGAGAGTGTGTGTATGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGAGTCCTCCACTGTGCTATAAAATACCTGGTTTTATTCCTTCTGTGTAACTGTTTGGTACCCATCATCTCGTCATCCAACCTCCCAGTGTTCCAGGGCCCTACCCCTCCCCTAGCCTCTGAAACCACTGTTCTACCTCCTGCTTTCTGTTAACTGTTAATGTTTCAAATTATTATACATTGTATTTCTGTTAATGTTCACTTCTGAACACCTCTAGTCTGTCTGTCCCCCTCCTCGTCCCTGCTCCCCAACCCCCCATCACCCATGCAAAGACAAGATGACTTCTTTATAACTGAGTGATGCTCCCTGTGTATGTAAGACACATTCTTTGATCACTTGGACGGACACCAAGGCTGACTCCACATCTTACCTATGTGGCCAGTGCAGTAGCCATGTGGGTGTGTAAGCATCACTCAGATACAACTCAGACACACTCAGAGGTGGAACAGTAAGCTTGTGTAGCACGTCCATCTCTGTTTAGTTTCCAGCATGGCGGAGCTAGTCTGCATTCGCACCAGTAGTGCCCCCTCCTCTCCAGCACGTCTTTCTGTCTCTCTGATAATGGTCCTGCTGGCTGTGATAAGATGATGGCCCACTGAGGGTTGGGTTTACATTTCCCTAATGATCCATGCAGCTGGCATGCTTCCATAAGCCTGTTTGTTAGTGTTTTTGCTTCTTTTGACACTTGTCTTCTGTCTTTCTAAATGAGCCTAGCCCATCTCAGGCCAAGGCAAGGGCCTGGCCTCAGGAGCGGAGAACCCCGCTTGCCTTGTTCCTTTGTCCTAGCCTTTTTGGAGCTAATAGGTCATTCAGAACACAGTAGGCCCCATGACCAAGTACTGCTTTGTTACTTTCTTTCTAG
Seq C2 exon
GGTCCCACTGGCCCGAAGGGCGAGGCAGGCCATCCAGGACTCCCTGGTCCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:60
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(18.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100)
Main Inclusion Isoform:
NA
Other Inclusion 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]