RnoINT0039996 @ rn6
Intron Retention
Gene
ENSRNOG00000008749 | Col5a1
Description
collagen type V alpha 1 chain [Source:RGD Symbol;Acc:70920]
Coordinates
chr3:6558232-6559699:+
Coord C1 exon
chr3:6558232-6558285
Coord A exon
chr3:6558286-6559645
Coord C2 exon
chr3:6559646-6559699
Length
1360 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
GTGTTCTTTCTCCTAACCAGGGA
3' ss Score
9.86
Exon sequences
Seq C1 exon
GGTCAAGATGGCCCACCTGGTGACAAAGGGGATGATGGAGAACCTGGGCAGACG
Seq A exon
GTGAGTGTGTGGTCTGATGGCTTTCTGGTGGGAGCCTCCCTTCATTTTCCAGTCTTTAAGAGAAGCCCAAACCTAGGTCCCTTTTGACTGTGGGCAAACCTCAGGAGCCCCAAGGACTTGGTGAAGTCTGGGACCCTTCCTCCAAAGGGAGGGTGCATATGCGTCCCAGCAGAGGACCCTGCAAGGGCTCTGCAGAGTACCCCACATCTCATCCTGAATGTCAGCCAGAGCTGACTGACTGGTGTAAAACCTCCCGTGACTTGGTCTTGAGCAGCTTTTTTAATGTGAAGTGGTCTCTTTGGGATGGGACCAGATGACTTCTTCAGGTCCCTGGGCTGCACTGCGCCTCTCTCAGAGGTCTCTTCAGCCCACGCCCAAGGTGGGACTAGCTCCTAGGAGGACTGACTGTCGAGGTCTTTTCACTGCTAATGAGAAGGTTGCAGACTGGTTGATTAAAACAAGATAAGTGTGTTGGGCTTAGTGCTACAGGCTAGAACGTCGGGATAGAGGGTGGGTGGGGGGGGTGTCTTGCTGTGGCTTAACAAGGGAAGAACAGATCTGTTGGCCCATGCTTCTGATTCCAGCACTCAGGAAACTGAGGCAGAAGGATTGCTGCAAGTTGGAGGTCTTTCTGGCCTACATAATGAGTTTAAGGTCAGCCTTGCTTTTAGAATCAGATCCTGTCTCAAATAGCAATACTGTAGTGGACGCCATCATGAAATTGGGAGGGGAGTTGGGCTTAACCCCCCCCTTTTATAATTCACTCACTTCTCCAGTGGTGTTGAAATCTAATCATACTCACGTGATCTGACAAGCAGGCCCCTCTGTCAATACCAGCACAAAGGCAATTTGATATATGAGCCTGGGTTTCAGAGGCCATCCAAACCATAGCACTGATCCAAGGGCAAATACTTGTGTCACTGGTCTGAGACAGGCAGCAGTGGAAACAAAGGGCTGGGGACACAGGCTGTGAGCCATACGTGTTCTGCCCATTCCCCTGTTCCCCAAGCCCCTTCCTTGGGCTCCAGGCTTGGTCCTTCTGCAAATAAGAGGTAGGAGGTGGTAACATGTTGGAGACCAGACAGCAGAGTGCCAGGTGCAGACCTGTCCCACGGGATCTCTTTGCTCAAGGTCCAGCAACTGTGGGATGTGAGTTGGATTCTCTGAGCGTCACCAATAGGACACAGGGTGTGAAGGCTGTAGGTACTTTGTTGTGGACTTGCTATGCTCATACCAGAGAGAAGGCCGTGCAGAGCTGGCCATGGAAATAGATTCCCGTGTGTTTCCTTGCCTGTGGGCAGCATAGTCGTGTGTCCCTGATGGGACGAATTTCTAATGCTGTGTTCTTTCTCCTAACCAG
Seq C2 exon
GGATCCCCAGGCCCTACTGGTGAACCTGGTCCATCTGGGCCTCCAGGAAAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008749:ENSRNOT00000012334:52
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(17.9=100)
A:
NA
C2:
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]