RnoINT0039953 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6507215-6508938:+
Coord C1 exon
chr3:6507215-6507307
Coord A exon
chr3:6507308-6508881
Coord C2 exon
chr3:6508882-6508938
Length
1574 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TCCTCCTCTTTTCTTTACAGTTG
3' ss Score
11.2
Exon sequences
Seq C1 exon
TTCCGTTTTGGAGGTGGTGGCGACGCCGGTTCTAAGGGCCCCATGGTCTCTGCCCAGGAATCCCAGGCACAGGCTATCCTCCAGCAAGCCAGG
Seq A exon
GTAAGTAATGTGGACCCCTGGGAACCCGTGTGATAGAGCTTGTCCCTGGTGGCTGTAGGGACTGAATGATTGTCTCACAGTTTGCCTGGTCAGGAACCTAGGGAAGGTTGGGTCCTCCATGTCCAGCTGGAGAATGCGGGGAACTTATGGAGAGTTTTCAGGGGTGTCCTGTCCATAGTTAGGGGTAAGAGGCATCTGGGCCTCTGTAGCTTCTCTGGCCTAGCAAACCCCTCTTCTGCCCTGTGCAGACACTCACTCTGTGCCATGGGACAGGGAAGCCAGTGATAAAGCCAGAGTTGGATGAGGCTCCGTGTGTGCGACTAGGTTTTCAGGCCTGTGCCTTCCCCGGCCAGCCTCTTAATCTGTGTGCACTTTAATAGAAACCAACTGAGAGAAGGGCTTTATGGTTTTTATAAAAAGATGTATTCTTTTTCCGTGAGTGAGTGTTTGCCTAAAGTGTGTCCCTAGTGCCCACAGAGGCCAGGAGAGGGCATCGGTCACTTGGGACTGAGTTACAGATGGTTGTGAGCCACCATGTGGGTGCTGGGAATTGAACTTGGGTCTTCTAGAAAATGTGCTCTTAACCCCCAAGCCATCTCTCCAGTCCTGAGTTTTTTATTTTATTTTATTTTGTTTTATTTCATTTTGTTTCCTGGAATGTTTTTAATTTTATTTATTTTATTATCGTGCATGTATTGGTATATTTACACAGTGCATGCCTGTGTGGGGAGGCCTGAGGTGAATGTCGGGTATTTTCCTCAGTCAGTCAGTCTCTACCCTTATTTTGAGACAGCGTCTCTCATCAAACCTGGAGCTCCCTGATTTGGCTGGGTTGGCTGGCCAGGGAGCTTCAGGAATCTGTCTGTTTTTGCCTTCCCAGGACTGAGGGTAGAGACAGATGCTGGAACATCTGGCTTTTTACACGTGTACTGGGAATCCTAACTCAGATTCTCAGGTTTGCGTGGCAAGCAGTTTACCAGCTGAGCCATCTCCAGCCCCCAGAGCATTTTTAAAGGCAAAATAGTCTTCCAAAATTAACATGGCGCTGTGGTAGGGGTTGTAACCCTGCCACAGAGCAGCTCTTTGGGAAGACAAGTTGAACCACACCAAGTAGGAGGACAGTCAGTGCATGACTGAGAGAGCCCAGGCCCCACAGGCTCTCCCATGTACCGTCCACACCTCTCTTGCTGTTGGAGAGAACTTTGTGCCTCTTCCAGAAGTGAAGTAAAGAATCCACAAGGAAAGTATAGGCCTCAGCTCAGCTCAGGAAGGGAGAGCATATTTCAGATTTGGTACAGGGTGGTCCACCTCTCCAACAGGGCTAAAAGGAAAGGCTTTAGGGACCCTGCCCACAGTGGGTCAGCAGGTAGCACTAACTTCTACCTCTGTGTCCTGCTTCCCTGTGGAGATGCTGAGAGCCCAGAATTGGGTCAGCGAGACTTTCTCTGTGAAAGTCTAGTCTTTTCTGTCCTGGGCTACTTTTCCTCGTGATCACGTCTCATAGAACAGGGGCCAGAAAACCAGGACAGGGCCAGGCAGAGTCTTTTTCTGACTTCCTCCTCTTTTCTTTACAG
Seq C2 exon
TTGGCACTAAGGGGACCAGCTGGTCCAATGGGTCTCACCGGGAGACCTGGCCCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:13
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(25.8=84.2)
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]