DreINT0078281 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34269053-34271118:-
Coord C1 exon
chr20:34270948-34271118
Coord A exon
chr20:34269224-34270947
Coord C2 exon
chr20:34269053-34269223
Length
1724 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAAT
5' ss Score
4.06
3' ss Seq
TCATCTCTTTGTCTAAATAGTGG
3' ss Score
6.98
Exon sequences
Seq C1 exon
TTCACGGAGGTTTCTCCGAATGGATGGAGTGGGGAGCCTGCAGTGTTTCCTGTGGTACCGGAGTGCAGAGGAGGCTGAGGCAGTGCAATAAACCATTTCCTGCAAACGGCGGACGCCACTGCGTTGGATCAGCATCTGAAACACGCAGATGTCAAGGCAAACCTTGCCCAG
Seq A exon
GTCAATCATTTTATATTTTAATTCCTTTAGGTGCTGCACTGTATGCAAAAGTGGTGTTTTCATGGATAAACCAGTGCAAGTGATAGATGTTTAAAAGATGTATTATTTTTTGGGAGAAGCCTGTGTCATTTTTAGTAAAAACAAAAATAAAATTTCAGACCAGCGCATCCCTAATTTTCATGTTTTGTGTGACGTTGTTTAAATAGCAAATCTATTTGCGCCACTTTGTTGATTTATGGGTGTGCTGGTCTAAAAAGGAGTTCTAAAAAGAAGTGTGTTAAAGCGCATCGTTGGCACGTTGCTATTTTGAGGAACCAAAATAGGCTGCGCCATTGACCAACTTAAAACTAGTCTAAAGTCCAGCGCAGAGTGCATTAGTTGTGCGCCTACACACAGGATGTTTAGAAATGCACAAATATATTTACATATAAAAAAAAAATAAAAGGATTAAAATTTTACAAAAATTTATATTTTCTATATAAATAATGCCCCAAATAAAATCCACCACCTACATGCCTTCACCTCAAAGGGCTTTTTTCAGTTTATTCATGACAGTTTGCATTTGTATAATGTTATTATTATTGTTAGTATTATTTATTATATGCATATTTATATTTGTTTTAATAAAAACAAGTTTAGATTTGTCCACCAGTTAGGTTTTGGAGACCTATGCATCACCATAAGGGGCGTAAGAACAAGATGTGTGTTTGGATATAACTCAGTTTTTTGACCACACTTCATTATTATTGTTCATTTATTTGTTTTCTGGAAATAAGAACTGAATTTAGAAATAGCTTTGAAACAAATCTTTGCATTAACAAACTAAATTAAATATGTAGGCTAATGGATGTCGTACAACATAGTTTCCTTTTTCACAAAAGTAAAGAAGTAAAGAGTAAAAGTAAAGTGAGAAAGTAAAGAGGCCAAATGACGGAGACTTGTTCTTTATTCTCGCTGCAGATGCTCTGTTTAGCGTTCAGTTTCTCTAAAGCGTTCAGTTTTTCCACTTTCCACAATTCACGCCATGTAAATAACAATTGTGCCATGGCGTGACACAACTGACTCTTAAAGAGAATGTGAGATGAGACTCTGATTGGTTTTATGCGCGTTATGCTCAAAACATACCCTTAACTCATTAAGAGAATAAGCACTAACCTTGTTAGATCATGCGCAATTTTTCCATCCTTAAAATAGCAAAAGTGGATTCGGACGTGCACTTAATGCTTTTAGAATTTGCACCTAGATTGTTAAAATAGATTGTTAAAATAGAGCCTTGAGTCAGAATTTGCGAGGGGTATGAGTTATTTTTAGATTTTTTTTTTCAACAAGGGCTTGTTAGACTTTATTCTTTATTAACCGAATACCCAATTAATATTTCTGAAGCAAATAAATTTAGCCTTTTTCTTTACAATAATAAATACAATACAAAAAGTAATTCATTTATTATTTCACTCATATTTTAAGGTATTTTTATTTTATTTATTTTTTATTTGTAATTTGTGTTTTTCACATTTTTATTAGCTTTTGAGGTTTTCTATTTTCTCTTTAGTTTTAATTTTTTTTAGGATTTGATATTTTAGTGTTAATACCTTAACTTATTTATTATTGTATCATTTGTTTTATTTTTCTGTACCCTAAGGAGTTCTTCTAAACAAAAAAAGCAATAATGTAGAGGCTCATTTACTCCGTTTTCTATTATTGTAATCATCTCTTTGTCTAAATAG
Seq C2 exon
TGGATGGTAGTTGGTCAGAGTGGTCTTCCTGGGAGGAGTGCTCTCGTACCTGCGGTCAGGGTAACAGAACAAGGGTGCGGACATGTAGTAATCCTCCTGCCCAGCATGGAGGGAGAGCTTGCGAGGGCAAAGCGGTGGAGGCCATCATGTGTAGCATAAGACCATGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:88
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=0.034
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=87.9)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTTCTCCGAATGGATGGAGT
R:
TGGTCTTATGCTACACATGATGGC
Band lengths:
327-2051
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]