RnoINT0039970 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6530498-6532949:+
Coord C1 exon
chr3:6530498-6530551
Coord A exon
chr3:6530552-6532841
Coord C2 exon
chr3:6532842-6532949
Length
2290 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
TCCTCTTTTTCTGACTGCAGGGG
3' ss Score
8.81
Exon sequences
Seq C1 exon
GGTGAAGACGGCTTCCCTGGGTTTAAAGGCGACATGGGAATAAAGGGTGACCGG
Seq A exon
GTGAGTGTTGTGGGCCTAGGATTTGGGCGAGAGACAAGCAGAGTGGGTTTGGGGACCTGCATGTAAGTCTTGGGTGTTCGGGACCACAGAACAGCTTATGAAAAAGGAGGTAAAGACTTCTGCAAAATCTTGGTCTGAGGACAGAGTGTCTGGAGCCCAGGGGCTCCGTTCAGTGCTCTCTAGCCTGCTCCCCAGTTTCCACTCCAAAGCCAGGGCAGCTCTCACCTGTGTTAACTCCAAGGACAACTGGGGTCATTGGCACTGTACCCTGGGTGCTGGATAAGTGCCTTCATGAGGACTGGGGATCCTGGACTACAGAGAAACTTGACTTCAGAGGACGAAGAAGAAAGGGGGGGACACCCCAAATAGGCCCATAAGCAAACCCCCGACAGATGTAGCTGGCAGGACCATGTGCTATTGAGGATCTGCAGTCCCTCCTGCCACCCTCCTAAGGGTTTGCTGAGCTCCTGGACCTTCCTGGTCCCCAAGATGCACCCAAGTCTCTTTTGAAGCCCGTGTAGCCCCAACACCCTGCCGCCTGATGTTGGGCCATGGGTGAAGCGCCCCCAGCCTGGCTGCTTTCTGATAGGTTGTTCATCCCAGCTCCAGAGGAAGCTGTTGGTACAGACAAGGGCATGGCTTGTTCAGGTAGGGGGTGCCCAGCCCAGCAAACCCAATGAACCGGGGGTTAACACTGACACTGAGGGCGGTTTCTAGGAGCTGTTTGCTAGCTCCTGCTGGGAAGTTTCCTCACCGCTTCAGAATAGCTCAGAGCCTGACAGAAGGTGACACACTGTGTGCCTGGAAGCCCAGCTGTTGTGCACACCTGAGTGCCGTCTGTCTGTTAGCTCGGGCCTGTTGTCTGCTTGTGTAATTACCCTCATAGCAGGCCCTGAAAATCACCTTTGCCCCACATTCCAGAACAAGAGGGCCCATACACTTGACCCTTTGCCACAACCAGACGTGAGAATGTCTGAAGCCACCCGCCGTCTGTCAGAGGAGGAAAATATAAAAGGGACTTAGCGTTCTCTTATCCTGCTGCTGAGGGTGACTGCCCCGGTCTCCTCCAAGTGAAGGATCCTCAGTGCCTCTGGCTGAGGGACAGAAGTCCCTTTGACTTCCCCTTTCTGATGACCTGGCACTCACAGTTAGAGTCCACTTAACTGAGGCATGAATGTGGTGGCACATGGCTATAATCAATGCCAGGAGACAGAGGCAGGATAGGCTTGAGTTTGCAGCCAGTATGGTGTTTATAAGGAAATGAATTGGAGATGATTTGGAAATGGGTGATAGATGACATACATACATACATACATACATACATACATACATACATACATACATACATACATACATAGTGAATCACACAAAAGGAACTTCCTGGGAACACAGATCAGTTTTCAGTAGATGAGGGTGAGTTGGAGCAGGTGCTATGGTTTGCTTTCTCTACGAATAGAGCCTCTGGACTTTCTGTGGGTGCTCAGATGTAAATGCATAAAGGATGAATGGGTTGAAGGTGCTTTCCAGGGATAGGGGCTTCTTAGCTCTGTGGGTCAGTTGGTGCTCAAGAGTTCTGAAGTCACTGGTCTCTGAGCAGTCTGTTCTGATGTGAGGATCATCCATCTGTCTGCAGCTGTTCAGGAAGCAGGTAGTCAGAGGAGGACTCAGCAGGCACAGGTCACTAAGAGCTCCAGGGATGCCATTTGGAGATGACCACAGTGCTTCTGTGGCCTGAGTGGGTCGAAGTCCCTCTTGGTTTAGGCATAGACTTCATGCCTGCAACCAGGAAGACTGGATGAAGTCTCTGGGTCTCCTGGGTGTGGGTATAGCCTGATCACTGCCAGTTGGGTAGAGGTCCCCCGGATGCCTCCTGAGGCTCCAAAGAAGGTGAATTCGGGACTGAGACAGTTGGTCTGGATCAACTAAGGACCTTTCATCTGGGTGGGCCTTTGAGGACATGTCCTGGAACGATTACCATTCCTTTAGAGAACCCAGACTAATACAGGGGCAGAGTGATTCACAGCCACTACTGCTAACCAATTATTTTGGCCAAGAGTTCCTTATCTAGACAGGGGAGTCAGGGAGCAGAGATGGCAGCCATGGTGGCCCTCAGCGCAGAAGGGTGACCTTGGATTTGCCACTGATTTTCAAAGAGAGGCCAGGCAAGTGCAGCTCACACTGTGCAGAAGAACATGCCTATTTGGCAGACCTACTCCAAGGTGGGAGGAGGGGTCAGTTTGGGGTGGACACTGGGAAGGATCTCCCTAACCTCCTCTTTTTCTGACTGCAG
Seq C2 exon
GGGGAGATCGGCCCACCCGGCCCCCGAGGAGAAGATGGTCCTGAAGGCCCAAAAGGTCGAGGTGGTCCCAATGGTGATCCTGGTCCCCTGGGGCCCACCGGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:29
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(21.8=100),PF0139113=Collagen=FE(24.6=100)
A:
NA
C2:
PF0139113=Collagen=PD(10.3=22.2),PF0139113=Collagen=PD(42.0=80.6)
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]