DreINT0078234 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34296241-34297767:-
Coord C1 exon
chr20:34297492-34297767
Coord A exon
chr20:34296409-34297491
Coord C2 exon
chr20:34296241-34296408
Length
1083 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
ATAAATTCATTTGTTTATAGTTC
3' ss Score
4.39
Exon sequences
Seq C1 exon
TTCGCCCCTCCATCAGCTCCTCGGCTCAGGATGAAGAGACAGTGACAAGAGGTGGTGATATTACTCTGCGGTGTGAAGCAGACGGGGTGCCCAGACCTGCCGTTTCATGGATGAAGGATGGTAGACCTCTGAGCACAGGCCGCAAGGCTCAAATACTTAATGAAGGCAGACTTTTACGCATCCTGGAAGCTCAAGTAGCCGACACTGGAAGATACACCTGTATCGCCATCAATGTGGCAGGACAGGCTGACCGGAAATATGATGTCAATGTTCATG
Seq A exon
GTAAGAAAAAAGTTTATTTCTGGAATTGCAAAGCAGCAGGGTGACTAGTTTTCCCATTTTCCTGTCACAGTCTCATATTTTATCACTACTTAAGTGTTCCAACTTAAAATAGTGTTTTTTTACTTAAAGTAGTTTATTTTACTTTGTCTAAAAATGCTGAACTACTCAGTGTGCATAGTGAAAGTAGGCAAAACTAACCTTATTGAAGGTATCCAGTCATGGTATATTTTGAAGAACAAAATTACTTTAAAAAAAAAGAGAGTAAACTTGTAAACCGCATCCCAAGTGAGACACTATACACCATATACTTATGCACTATGTATTTTGACACTTACAAACTCAACAGTATAGTATATGAATGTAGTGCCGTCCCAAATGGGGACTAACTTTACTAACGTTTCCCAAACATTGCCATATTAGCAAAATAAATGACCAAACTACCAAATAATACCTGCCATGAGTATAACCGCACTCACCATCGGGAGGCGCAATTATCACTATTGTTGGAGAATTTTGCTTTCACAATACAAAATAAATGAAGAAATACAGCATCAGTGCCCGAAAGCTCCACCCCTTCAACCTCATGATCAAAGCTGCGGCCGTTGAGTGCGTAGAGTGTCCAACATTCCACACTTATTATTAACAGTTGAATAAGTGCATCATCTGGGTATTTAAAGTGCACTTATTCTTTTTAGAGTTTTTAGTGTGAAAGCACTACTTACACTATTTATACTACAAAATGGCATAGAATAGTGCATAGGTGTGTGATTTGGGATGCACCTGTTGCCTAAGTTATTAAGTATTATTAAGTAAACAAACTATGTACATAATTATAAAAGTCAATGGGTTTGCTGATATTTTAAAAAAGTAAAATCAACTTGTTGCTTTTTAGGCAGCAAGTGTACAAACTTTTATAAAGTAAAGTAACTAAACTGCTTTTTACAGTGCAAGTTACCTTGAATTTTACCTCTCTTGCAAACATAAATCCTTTTCTCAGTGTTGTTTATATTGTTTTTTTATTCAATATGTATGTATATATTTTTTGTTATAAATATATAATACAATAAATTCATTTGTTTATAG
Seq C2 exon
TTCCTCCCACCATCATTGGCCAGACGCATATGCCTGAGAACATAAGTGTTGTTGTGAAGAATCCAGTCGTTCTCACTTGTGAAGCTTCTGGGATGCCCCCACCTGCTATCACGTGGCTCAAAGACGGCCAGCCGATCAGCACATCTAGCTCTGTTCGGGTCATTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.204 A=NA C2=0.123
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=95.7)
A:
NA
C2:
PF0767911=I-set=PU(57.0=86.0)
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:
CCTCGGCTCAGGATGAAGAGA
R:
GGCATCCCAGAAGCTTCACAA
Band lengths:
355-1438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]