BtaINT0042270 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019081 | COL7A1
Description
collagen, type VII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2214]
Coordinates
chr22:51885846-51886228:+
Coord C1 exon
chr22:51885846-51885926
Coord A exon
chr22:51885927-51886174
Coord C2 exon
chr22:51886175-51886228
Length
248 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGA
5' ss Score
6.03
3' ss Seq
TTACTTCTTTTTTCTTTCAGGGT
3' ss Score
12.47
Exon sequences
Seq C1 exon
GGATCCCCAGGAAAAGACGGAGTCCCTGGTGTCCGAGGAGACAAAGGAGATGTTGGCTTCATGGGTCCCCGGGGCCTCAAG
Seq A exon
GTGGGAAGGGGGCTGGCTTTTTTTCCCCATAATCAGGACCTGATGTTGGAGGGTGAAGTATCCAGGGTCAGAGGTCAGGTATCTGGGGTCAGATGCTGTGGTATCTAGGGTTGAACGTGAGGTGTTAGGTCAGAGGTGGGAAGGTCAGAGGTTGGAGTACCTAAGGGCAGTTTGGAGAGGGGTTTCAGGGTCAGGGGTCATAGGTGAGGTATGTAGGAGGTCACTTTCTTACTTCTTTTTTCTTTCAG
Seq C2 exon
GGTGAACGGGGAATTAAGGGAGCCTGTGGCCTCGACGGAGAGAAGGGAGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019081:ENSBTAT00000025418:105
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(39.4=100),PF0139113=Collagen=PU(10.1=29.6)
A:
NA
C2:
PF0139113=Collagen=PD(16.7=61.1),PF0139113=Collagen=FE(21.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCCCCAGGAAAAGACGGA
R:
ATCTCCCTTCTCTCCGTCGAG
Band lengths:
132-380
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]