RnoINT0039979 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6542269-6545222:+
Coord C1 exon
chr3:6542269-6542322
Coord A exon
chr3:6542323-6545168
Coord C2 exon
chr3:6545169-6545222
Length
2846 bp
Sequences
Splice sites
5' ss Seq
ACTGTGAGT
5' ss Score
7.94
3' ss Seq
CTGCCTGACTCTCTCCACAGGGT
3' ss Score
12.36
Exon sequences
Seq C1 exon
GGTCCACCAGGCAAGGACGGGCTCCCCGGACATCCTGGGCAGAGAGGGGAGACT
Seq A exon
GTGAGTATTACAAATGCTAGGGACATGGTTGTGCCTGGCCTCCCTGGCTGGGACTCCTACAGCTTACAACATGCGGCTGGCTGCTGGCACAGTCAGGGGATCCTTCCTCTCTGGGAAAGACCAAAGGCCTTAGCAAGGCTTCCTGTGGGCCAGCCATCTGCTGTTGACTTAAGGTCAAGCTGTCGGGTGGGTGGGAGTCCCATGATGTCACAGTGAAAACTGGACAATGGCTGTTTGCGTGTTTTAGCGGCTTTGGCCAAAGACCATGTTTAAAGCATCAGGACACAGTGCATTGGCATCACGAGATCTGGGTCTCCAACCTTTATTTAATGAGGGTAACTGAGTGTAGCCTGGCTTGGGACACCACAGGCCTTACTTGGAAGAGTACCTGGGGAGGCTCTGTACTTGTGGATAGCTGGTTGTTTAGGCTACAAACCTCATGACGAGGGCCATGGGCCTTGGGTCTCACACAGATCCCAGCTTTGTCTGTCTGAGAGATTTCAGCCCGAGGAGCTGGCAGGAAGGAGCAGGGTGAAGTCTTTATCCTCCTCTGTAAGGAAGATGCTGTGCAGGAGAGATGAGATGGCTCAGTGGGTAGAGTGCCCGATGGGACAGATATGAGGATCTGAACTCTTCCCGGCACTGGTGTGAAAGCTTAGCAGGGATCCTGTAACCCTGGTGCTGGAAAAGTGGACCAGAGGATTCCAACGAGGCACCTCTGGTTCAGGAAGAGACCCCATCTCAAAAAGAGCATGTGCACATTCGTGACCTTGCTTGCACTTGTGACCCTGGGGTTCCAGACTTTGAGTGACTGAGCCCTGAAAGTGCGGGTGACACCTGTGTGTTCTCTTTGTGTGACCCTGCCTCATCCACATTAAAGACAGTCTGTGCCAGTGTAAATGTTTCTCCCTGACAGCCTCCTGTGTCATGGCATCCTGGGCCATGGCATCCTGTTCACTGTGCTGGGGTTGGGGTGGGGGCTCTCGTGGCTCTTCGACCACCCTGCCCGTTTCCTGGTACCTGCTTTAACACTTGTTAAGGTGTGAAGTACCTGCTTGTGCCTGCTCCCCCATCCTCCGTCTTTCAGCACAGAGGGATGTGAAGTCTTTTAATTATGCCTTTGCTGGTGTTCAAGCAGCCTGTGCTGGCTGATAAATGAAGATTACCTTGCTCTTTTGTTTAGAGAAAAAAATTAAAACATTTCTTCAGAGCTTTGCGCATTTTCCTCTAATGCCTTTCCAAGGAGACAAGAGAAAAGAGTTTTGCATACTGCAGGCTTTCCTCCCTCACACTCACTCTGCAGATAATTAAGCCTCCTGCTTTGCTTGGGAAAGTATAGTTTCCAGCAATTTCTACCGTGTCCAGCTACCTCTGCAGAAACAGGGGTGCTGCGTGCCGCTGCTGGCCATCTTGACCATCTCTGAGACTCATCTGAACGTCTCTAGAGTAGACTTCCTTGTTTTCTTTTTCCTCTCCTCCTTCCTCCTCCTTCCTCCTCCTTCCCTCCCTTCCTCCTCCACCTCTCCTTTTTTTCTCCGACTTCCTCCTCCAATGAACACAAATGGCTGTTACTTCTCCTTAGTGGGAGCCAAGAGCCTGTTTCTCAATGAGGAGCAGAAGACCAGCTCTCTCCTTATCCTGTCACCCTAGAGTGACTGTGGCCAGCCAGCAAGTCTAGCCAATGGATCGATTCTGAGTTCAGAAAGAGACCCTATCTCAAAAAGAGCATGTGCTTGCTGGTGGCCTTGCCTGTACTTGCAAACCTGGGATGCCAGACTTGGAGCAACTGAGCCCATCAAGTGTGGGCAACAGCTGTGTGTTCTCTTCGTGTGTCCCTGCCTTGTCCACTTGACAGGGAAGTTGGCTCCTCTTGCCCTCTCTGCTAGCACTGTCACAGTGAGCAATTTTGGCTCCCATGTCCCATCAGACACTTCTCCCTCTTGACTTCTCCTTCGCTTTTTGCTTTTGACTGTTAGAGAAATGTGTCTTAGACATGGCCACTTCTGCCCACTGTGTGAGTTGGGCTGAGAGAGAAGAGCCCTCTGGGCTTTTCAGGGTAGAGTCTGCTGTGGTTCCTGTGGCCGGTGAATTGTGTGTGATAGTAGACTGTTGCCTACTGGTCTTGAGCCATCTGCTTACCCTCACGCCATAGTTATGACCCCTGCACAGCTAGAATGCCCTTCTCAGGCCTTAGGTAGATCCACCGTTGGATACCCGGCAGCTGCCGGTGTATCTCATTGTGCCTACTTGGCTTCAGCATCGTGCCCCAGATCAAGCTCAACTCGCTGCAGCTTCCAGCTCCATAGGAGAGCTTGGGAAGCAGAGCCGAATTGGATGAGAGCCTGGGCCATTCTAGGCATGAACACTCAGATCCTGGAGAAGACAGGGTCTATGAAGTGACTTTAAAGTCACACGTTGGAGCTGACAGCTTCAGAGAGCAGTCAGACCTTGCTTCAGCCTGTCCTAAATACGGAGAGGAGCAGGCCGGCGGCTTACCTGCCGTGAGTCAGAGGCGTGGATAACAAAGGCTAAAAAGTCCCACGACGTCGTTAATGAGCACCAGCCCAGAGATGGTTCTTACGTGTCCTCAGAAAATGAACACACGGTGACAGGAGGGGGGGAATAACAGGCTTACAAATCCATTTTTCAGCACAAAGACACAGCGTGGAGCTAACCCAGTCGGCTCCAGCACTTCCATGAAATTAATATGGGAAGGGAGCAAAAGGCATGACTCTAAACTGAGAGTTTGGCACACAGCCATTGGGGACAGGTGGGGGACGGGCTTGTGAGACAGCAGCAGGATGGGGCCGCTGCAATGGCCCTCAACTGCCTGACTCTCTCCACAG
Seq C2 exon
GGTTTCCAAGGCAAGACTGGCCCTCCAGGCCCTCCAGGAGTGGTTGGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:37
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(23.6=100),PF0139113=Collagen=PU(11.6=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(19.4=77.8),PF0139113=Collagen=FE(17.9=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]