DreINT0078192 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34260544-34261416:-
Coord C1 exon
chr20:34261291-34261416
Coord A exon
chr20:34260673-34261290
Coord C2 exon
chr20:34260544-34260672
Length
618 bp
Sequences
Splice sites
5' ss Seq
TAGGTTTGT
5' ss Score
4.07
3' ss Seq
ATTTTTTTATCTGCTTGCAGACA
3' ss Score
9.73
Exon sequences
Seq C1 exon
ACATAAATGAATGCAAACAGAGAGTGTGTCGCTCAGATCAGCAGTGTAAAAACACACGTGGTGGATACACTTGCATTGACCTCTGCCCTACTGGCATGACTAAAGGAGGCAATGGCACATGCATAG
Seq A exon
GTTTGTTGCTTCTGTTTGTGGAAGAGGGCTATTGTGATTAGGGCTGCACGATATTGGAAAAAATCTAACATTGCAATATTTTGTTTTGCTGCAATATATATTGTGATATGAATATAATCTCTCCAGAGGATTTAAATAAATTTATATGGAAAGATTTCATTCATTTAGATTGACTAGGATAAGTGATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAGCTATTGTGTGGAATATTCAAGTACAGAAATTGAACAATCATATGTAAAAAACACGGTCATCATTGTATAAATAATAATAAAAAATACGAATATTTATGAATTTCTTATACAATATATTGTTCAGCCCTAATTGTGATGCCCAATATATATTTTTATTATAATATTTATCTTATTTGAGAATACACTTAATATATTCTATATGAATAAAATATTCTGATAGACATTGTATTTTATTATACATGCATGTAAAAACATTTTTAAAAATTGTGAAATTTTTTTTTTATATATTTTATCGTTATCGATAACATTTATTGCTACAAAATGAGAATTTAATCAAAAACTAATACATTTTTTTATCTGCTTGCAG
Seq C2 exon
ACATTGATGAGTGCCATGACGGCACACATCAGTGCAGGTATAATCAGATCTGTGAAAACACCAGAGGTAGTTACCACTGCACCTGTCCGAGAGGGTACCGTTCTCAGGGTGTGGGACGTCCCTGCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:102
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:
PF0764510=EGF_CA=WD(100=95.3),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATAAATGAATGCAAACAGAGAGTG
R:
GACGTCCCACACCCTGAGAA
Band lengths:
246-864
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]