DreINT0037009 @ danRer10
Intron Retention
Gene
ENSDARG00000099412 | bcan
Description
brevican [Source:ZFIN;Acc:ZDB-GENE-030131-6045]
Coordinates
chr16:29380972-29382987:-
Coord C1 exon
chr16:29382880-29382987
Coord A exon
chr16:29381131-29382879
Coord C2 exon
chr16:29380972-29381130
Length
1749 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTTACCTTCTGTCCACAAAGATC
3' ss Score
6.65
Exon sequences
Seq C1 exon
ACGCATGTTTGGAAAACCCTTGCAAAAATGGAGGCACCTGTGTGGACAGTGGAGGAGATCAAAGGTGTCTCTGTTTGCCTACCTATGGAGGAGACTTCTGCGAGACAG
Seq A exon
GTGAGTTACCTTGTTATAAAATCAGTAAATCTTATGTTTATACAGTGGAAGTCACAATATATAAGATAAGAACAATAAATAAGCACGTTTTTTTATATAAATGCATACTGAATATTAATGTGAATGAATATTAGTTGTGCCTAGTCGAACCGTTTAACAAAATAACCGAAAATGACAAAAACTCACTCTCACGTGGTCCAACCTTAATGAATTTTTTCTTCTTCTGTTAAACACAAAAGAAGATAGTTTGAAGAAAGCTGAAAACTTGATTGCAGGTTTCCATCTTTCTTCCAGATCAACAGAATAAAGATTCAACTCATAAAAGTTTCAAACAAGTAAAGTACATTAATAGTAAACAGCAGAATGTTTGTTTTTGAGTGAACTATGCCCTTGAAAATTTCAGTTATCAAAATTGGAGAACAGCAAAACGAAGTTATAGTTTTTAAGTTTACATGAGTCAAAAATGAGCAGGAAGTGTAGAGGCCCTTTCTTTTGGCCACCCTAGGGCATACCTAGTCTAATGCTCTGGTTGATTTTGCTCCAATCTTCATCAGTCTCTTTCAAAGTTCAGTGACTTTGAGTACTTTCTTAGCCTGGACTTTGTCAGCATATAAATGTTTTTTAGCTTCTGTGATCTCGTCATTGAGAGACTTTTTTTAAATCACATATACATAATTATGTAAATAAGGATTATCAGCTAATTATGAAATTACCACCTGGTGCCAGAATACCTCCAATAAGTGGAAGGTGTCTAAAGTGTTGTCTAATTTTGAGCAATTATGCTAAATATGCAATTTAATATGCTAGATTTTTTGATTAAAATATCCAAAAACCATGGGTTACACAATGGCTCAATGGTTAGCAATTTCGCCTCACAGCAGGACGGTCGCTGGTTCGATTTCCAGCTAGGTCAGTTGGCATTTATGTGTGCATTTCTGTTCATGTTTTTCCCATGTTGGCGTGGGTTTTCTCCGGGTACTCTGGTTTCCCCCACAGTCCAAAGACATGTGCTCTAGGTTAATTGAATTAACTAATCTGGACATAGTGTATGTGTGTGAATGAGTGTGTATGGATGTTCTCCAGTACTGGGTTGCAGCTGAAAGGGCATCCGCTGTGTAAAACATATGCTGGAAAAGTTGGCAGTTCATTTCGCTGTGGCGACCCCTGACGAATAAAGGGACTAAGACGAAGGAAAATAAATGAATATCCGAAAAACCACTAGAACGGTGATCTCAGATGTTTCAAATCCAGAGAAATAAGTCATTCAAACTAGTTATACAGACGGTGTCCTCTGTGGCCATGCTAATGACGTCACTTACCCTCAATTTCTGGTTTGGTTATATAAAAAAACAGGAAACACATACTGTAGGACACTTTAAAATTTTGTGTTTTATTAGACTTTACAGAGTAGCATTATAGCAGAACTCTATTGTTCTGCTATAATGTAAATATATAAAGTACTATAGCAGATTGCGTTAACGAGCAGTTGGACAGGTGTACCTAATAAAGTGGACAGTAATTATATGTAAATCGTGAAATATGCTTTAAAAATTGTTTGTTTACTCCTGTTAAAAATAAACTGATAACTTTATATAGGACTTTATTTGTTTTTAAAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTAAGCTGTACATGCTTTATATTAAAAGTCACACTCTTACCTTCTGTCCACAAAG
Seq C2 exon
ATCTAGAGCATTGTGAACCAGGCTGGGAGAAGTTCCAGGGGTTTTGCTACAAGCATTTCGCCAAGCGTCAGAAATGGGAAGTGGCAGAGCAGCACTGTCGCATGTGCGGAGGTCACCTGGTTTCTGTTATGTCACCTGAGGAACAGTTGTTCATCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099412:ENSDART00000162835:9
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:
PF0000822=EGF=WD(100=83.8)
A:
NA
C2:
PF0005916=Lectin_C=PU(30.2=59.3)
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:
ACGCATGTTTGGAAAACCCTTG
R:
CTGTTCCTCAGGTGACATAACAGA
Band lengths:
254-2003
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]