DreINT0049951 @ danRer10
Intron Retention
Gene
ENSDARG00000012593 | col5a1
Description
procollagen, type V, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-041105-6]
Coordinates
chr21:6770375-6771226:+
Coord C1 exon
chr21:6770375-6770482
Coord A exon
chr21:6770483-6771172
Coord C2 exon
chr21:6771173-6771226
Length
690 bp
Sequences
Splice sites
5' ss Seq
GTGGTGGGT
5' ss Score
4.29
3' ss Seq
TCTATCTGGTTTTGATGTAGGGA
3' ss Score
7.67
Exon sequences
Seq C1 exon
GGTGAATCTGGTCTGGAGGGTCCGCCTGGTAAAACAGGTCCAGTTGGTCCTCAAGGAAGCCCTGGAAAGCCTGGTCCTGAGGGTCTGAGAGGTGTGCCTGGACCAGTG
Seq A exon
GTGGGTGATATCTAAAACTATATACAGACATACTGTGATATTTAAAAAAAGAATCTAAATTTTAGATAATTGTGCCTTCAATTGTAAACATTGTTTACGCTCATATATACAGATATGAATTCTACTATATTTAATTAAAGAGTTCACCCAAAAATAAAAATTATATCATCATTTACTTCAAACTTGCTTGAGTTTCCTTTTTTTCTGTTGAAGACGAAAGAAGATATTTTGAAGAAAGTTGGAAACCATTAACCCATATGTCTCAAACTAGATTCCTGGAGCTCTGCCGTTTTGCTCCAACCCTAATCAAACACAGCTAATCCAACTGATCAAGATGTTCTAGACTACTATAGACTATTAAGCAGGTGCGAGTTAGAGATGATTGGAGCTAAACTATGCAGAGCTGTGGTTTTTGGATGGATGTCAGATTCTAACTTTCTTCTAAATATCTTTTTTTGTCTTATATAGGTTTTAACAAGTAGAGGATGAGTACAGTAAATGATGAGTACAAGTTCATTTTTGGGTGAACTATCCCTTTAATCTACCTTCATTCGCAATGTCAAATTAAATATAGAATCAGAATCGCCCTTTCAGCCTCTGAAATGTAACCGCAGACCTCACATACAGGTCTTTCTAAAGCTGGGATTCTGATTTGGTGCTAATGAATTAATCTATCTGGTTTTGATGTAG
Seq C2 exon
GGAGAACAAGGACTGCCCGGTGCTCCTGGACCCGATGGACCTCCTGGACCGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012593:ENSDART00000139598:54
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=PU(39.7=80.6)
A:
NA
C2:
PF0139113=Collagen=FE(22.0=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]