GgaINT0139608 @ galGal4
Intron Retention
Gene
ENSGALG00000013237 | BCAN
Description
brevican [Source:HGNC Symbol;Acc:HGNC:23059]
Coordinates
chr25:502899-505075:+
Coord C1 exon
chr25:502899-503330
Coord A exon
chr25:503331-504967
Coord C2 exon
chr25:504968-505075
Length
1637 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
GGGCTGCCCATGCCTTGCAGGTG
3' ss Score
8.21
Exon sequences
Seq C1 exon
ATATCCAAGAGCCATCCCCCTCCATAGGCAGCCGTGGGGCCGGGGGGGCGAGCACCCCCATCCACACCGCGGGGGCTGCTGAGGACCCTGAGCTATCAGGAGATGTGACTGAAAACCCCGGGGCATCCCCGCTGCCCCCCGCACCGCCGCAGCTGCAGGATGATGGAGAGGAGCAGTCGGGGGCCCCGTGGCTCTCCTCACCCACAGCACCGGGGGATGGGGGCACAGCCCCAGCGACGGCGGTCACCCCATGGCACGCAGAGGTGCCCGGCAGCAGCGATGCACTGCAAACCCCAAGCACCGATCGCGGGATGCCCGCTGCATCTTCAGAAGAGGAGGAGGATGAGGAAGAGGAGGAGGATGAAGAAGAGCGCCCGATGCCCTCTGTTGCAACCGTGGAGGGTTTCCTTGCAGCCATTCCCGGAGAACCAG
Seq A exon
GTGGGACCCACAGGGACGGCCTCACCTCTCCCCATGCTGGGCCCCCCAGGCTGTCCCCAGCACCCAGCTCGGCCACCCCACTGCCCGCCCTGCCCACGGAGCGTGCCAGCCTGGGTGCAGGTGCAAGCTTGGCCGGGGGTCCCCGGCACTGTGTCACTTTTGCACTCGGGGCAGCGCTCCTGGCTGCACGCTGGCACTAGAGAGCGGCAGCACCTTTCCTTTGCACTTTGCTTTCCTCTCGTCTGTCTGTCCTTCTGTCTGTCTGTCTCTCTCTCCTCCTCTCTTCGGCTGGGTAAGGGAAGGTCAAAGGTCCGGAGAAGCACATATTTGTCAAACAAATTGGTCTGAGCTATGCATGCACTTAATTCTCTTCTACTTCTGTGAAGTGTTTTAATGACTGTTTCCATGAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAGAAACAAATCTATCAAAAGAAGGCCCCAAACCCTCCTCTGACTAACAGTGGTACTAATAAAGGGAATTAAAAGCTTTCTAGAACATGCACCTCGGCTAGCTCTTCCCTTCATCCTTGCGCCCGCTGCCTCGCTCGCATCCCCACTGACGAACTAATCCCCCTGGGCCCCAGAGGGATGAGGACCTTTGGGGCTGAGCACGGTGTGAGCTGTCCCTGGAGCACCCCCATGGTGCACGCAGCTGAATGCCGTGCAGAGCTGTGGGGTGTTGGGTGTTCTGGGGGCGCACGGCCTCAAGGTGAGCACCAGGGGCTGAGGTGGAGCCCACTCGCTGCAGGAGGGTGGTGTGGGTGCATGAGCAGTGACCCCAAGGCGAAATTCCTCTTGGCTCCTAAGTCAGGATGCTCTCAGCTCTTCAACCAAACCCCTGCCCATCTTGCTGCCCCTTGACCCTGTAGGACAGCCTCGCTGGGGGTCCTTTCTTCACCCCCCCAGCATAGGCGCTGCTCAGCACCTTGCAGTGTGGATGTGTACGTCCTGGCAAGAAGAGATGTGCTCTCAAAGAGCCGGATGTGCCCAAGCCTTAAATAGATCATTTCTCACCCTGCTGCAGTCCACTGGAGATGTCCGCATGTCCCTGCAGGCAGGGAGGTGATGCTGTCTGGGGCGAGCGAGGGCACAGGGCCATTGGATAGTGCCAAGGACTTGCACTCTCTGTGCCGCCGGCGCTGGCGACAGCCCTTAATCACATTCTTGAGCTGGGGACGGATTAATGACCGTGTGTCTTAATGACCGGAACGGGCTGGTGCTGGTTTTGCAGGTCGGGGATGGCATCACTGAGTTCTCAGCCTTGGGCAGGCTGAAGGTGACAGCAGTGAGGTTGGGGACGGGCACGAGGCTCGCCTTGCTGCCAGGCTGAGGACGTGTGGCTGGGACATGCCAAGGGCTTATCCTTTCATGTTCCCTCCAAAAGAGCCATCGTTGCACTGCTCCGGGGGCAGCAGGACTCATCCCCATCCACGGCACACTCTAACAGAGTCCAGCTGAGTGCTGGGGACATGCCAAAGCCTCAAACCCATCCAGTGCAGGAAGATGGGATGGCTCCAGCCGTGCCACCGTGCCCCAGATGCTGTGCATCCATCCGAGGGCTGAGGGGCAGCTCGGGGGCGTGCAGTGAGCAGGGCTGCCCATGCCTTGCAG
Seq C2 exon
GTGGCTGCATCCCCAACCCCTGCCTGAACGGAGGGACCTGCATTGAGGATGGCACCCATCCCACCTGCCTCTGCCTGCCAGGCTATGGAGGGAGCAGCTGCGAGAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013237:ENSGALT00000021615:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.972 A=NA C2=0.054
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=83.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTGCAGGATGATGGAGAG
R:
ATGGGTGCCATCCTCAATGC
Band lengths:
342-1979
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]