GgaINT1007243 @ galGal4
Intron Retention
Gene
ENSGALG00000013237 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:HGNC:23059]
Coordinates
chr25:498854-499443:+
Coord C1 exon
chr25:498854-498946
Coord A exon
chr25:498947-499050
Coord C2 exon
chr25:499051-499443
Length
104 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
CTCTGCTCTTCTCCCCCCAGATG
3' ss Score
13.39
Exon sequences
Seq C1 exon
GGCACAGGATGGCCTCAGTCCTCCCACTGCTGCTGCTCTGGGCGTTTGCCCCCACAGTGGTCCCGGAGGTGCTCAGCCCTGAAGATGTCACAG
Seq A exon
GTAACATAGCTCACCCTCACACCATAGCCAGTATCCAGGGCTGGGGGGGGGGAAAGGGGGTTCACACGCCAGCCCCACTCACCGCTCTGCTCTTCTCCCCCCAG
Seq C2 exon
ATGACCTCAAGGCCCTGCAGGTGTCCATCCCGCGGCACCCAGCCCTGCACGCTGTGCTGGCAGGGGACGTCACCATCCCCTGCCTCATCACCTACCTCGCACCCCTGCCCACTGCCAGCACGGCGGGGCGCCGGGCTGTGCTGGGAGCCCCCCGGGTCAAGTGGACCTTCATCTCCGAAGGCAGGGAGGCAGAGATCTTGGTAGCACGGGGGGAAAGGGTGAAGGTGAGTGAGGACTACCGCCTCCGTGCCTCCTTGCCAGTCTTCCAGCAGCGCTACACTGACGCCTCTCTGCTGCTCACTGAGCTGCGCCCCAACGACTCGGGGATCTACCGCTGTGATGTGCAGCACGGCATCGAGGATGGCCACGACATCCTCGACCTCAGAGTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013237:ENSGALT00000021615:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0768612=V-set=PU(92.7=96.2),PF0019312=Xlink=PU(0.1=0.0)
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:
GCTCAGCCCTGAAGATGTCAC
R:
CACTCACCTTCACCCTTTCCC
Band lengths:
254-358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]