RnoINT0040326 @ rn6
Intron Retention
Gene
ENSRNOG00000020579 | Col7a1
Description
collagen type VII alpha 1 chain [Source:RGD Symbol;Acc:1311417]
Coordinates
chr8:117695170-117696225:+
Coord C1 exon
chr8:117695170-117695350
Coord A exon
chr8:117695351-117696065
Coord C2 exon
chr8:117696066-117696225
Length
715 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
ACCCTGCTTTCTCCCCTCAGGAC
3' ss Score
13.1
Exon sequences
Seq C1 exon
TGACCTGCACCCGCCTTTATGCTGCTGACATTGTGTTCTTGATTGACGGCTCCTCGTCCATTGGCCGCAGCAACTTTCGAGAAGTGCGGGGATTCCTGGAGGGGCTGGTGCTGCCTTTCTCAGGAGCAGCCAATGCACAGGGCGTCCGATTTGCAACAGTGCAGTACAGTGATGATCCACA
Seq A exon
GTGAGTAGCTGACTTGGGGGTCAGGACTGTAGGCCCTAAGACCCCTTGACAGGAAGGAGTCTAGAAACAGGGTTTGGAGAGCCCAGAAAGGCCCTCCTAGCCAACACTCCCCTGCAGAGAGGTAGGGATAACTTGAAAGAGTGGTTTTGTCTTAAAACACCCCTCAGCCCACTGGGGGGTGGTCCTGGGGTAGAGGTGGTGGGGGATGGACAGGATAGTTCTGTTTTCTGATCTACATAGAGAAAAGGAGTCCAGGAGCTCCAGGTATTGGGCTCCTATTGGAGTCTGCATGTTTGGGCTCTCCATTTTGTCTGGCCAGTGTTCACTGTCCTGAAACTGGGTCCTTCCTCCTATAATTATTATATAATCAGATATCCTGTCCCCGCCCCCCCTTGAGGGTCCCAGGCTCATTAAGGCTCAGTGACATTGATGTGTCAAGTAGCACCCAAGGAGGCTGTTAATGTGGAAGCTTCCGTGGTAGAAAGTTGGGGTCTCGGAACCAAGGGTACTCTTAAGAGGTCTCATCTCGGGGCTGGGGATTTAGCTCAGTGGTAGAGTGCTTGCCTAGGAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGAACCAAAAAAAAAAAAAAAAAAAAAAAAAGAGGTCTCATCTCAGAGGCAGGGCTGGAAAAGGTCATGGCCCCTTGCCTTGTGCTACCCTGCTTTCTCCCCTCAG
Seq C2 exon
GACAGAATTTGGTCTGGATACACTTGGCTCTGGGGGTGACACCATTCGTGCCATCCGGGAGCTCAGCTATAAGGGTGGTAACACTCGAACGGGGGCTGCTCTTCTCCACGTTTCCGACCGGGTCTTCCTGCCTCATCTAACACGTCCTGGCATCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020579:ENSRNOT00000027994:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=PU(29.3=83.6)
A:
NA
C2:
PF0009223=VWA=FE(30.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTGCACCCGCCTTTATG
R:
GGGATGCCAGGACGTGTTAGA
Band lengths:
336-1051
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]