DreINT0078194 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34256454-34258637:-
Coord C1 exon
chr20:34258275-34258637
Coord A exon
chr20:34256574-34258274
Coord C2 exon
chr20:34256454-34256573
Length
1701 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATT
5' ss Score
7.27
3' ss Seq
TCCCCATTTTGTGTTTGTAGATA
3' ss Score
9.23
Exon sequences
Seq C1 exon
ATATAAACGAGTGTGAGCTGGTACCGGTGCCCTGTGCCTATCAGTGCGTGAACAGCCCTGGCAGCTACAAGTGCCTGTGCCCACCGGGGCTCCACCTGTTGGGCGATGGCAAGTCCTGTGCTGGACTAGAGCGCTTGCCCAGCTATGAGACTTTCTCATATGGGTACAGAACATCCCAGTCCTCCTCTGATCGGAGCTCCTACCTGCAGCGATACCATAGCCTGACATCCCAGAGTTACCACTCATATGTACCCAATGGGGGGCGTCATGTGGCCAACAGACCCAACAGTGCCCCTTCACGCAATCGTAGGAGTACTTATATCTGTCCTCATGGTTTTAAGACCAAAAATGGCCATTGCTTAG
Seq A exon
GTAATTACACATGGTTAATCTGTAACTGAGTGTGGGTTTCATCTCATGTGTTATGTATACTGTATGTAAGGCACTCTTAAAATTAGTTGAGTCTTCTTTTTCACCGAAAACTAATAATCAAATGTCTTAAATCATAGTTTTCAAACTTAATTCCCGGAGGGCTGCAGCTCTGCACGGTTTTCTCCAACGCTGATCAAACACAGCTGATCCAAATAATTGAGGTGTTCAAAAGAGTCATGAACACCTTCATTAGTTGGATCCGCTGTGTTTAATTAGGGTTGGAGCAAAACTGTGCAGAGCTGAAGCCCTCCGGGAATTGAGTTTGAGACTTCTGTCTTAACGGAATAGTTCATCCAAAAATAAAAACTCATTATGTTTTTGAGATCAAGACTCATTATGTTTTTTTATTATAATATTGTATAAAAAAGTATTTTAAAGCAGTTTTTATAAAGTATCTCACTCATATTGAATAATTTTAAAAGAAAGAAGTCAATCATTACAATACTGTCAGTAAAAAACTAGGTAACACTTTTATTTGATGGTCCCTATTGCACATTTTGTTGATTTGCAACTACATGCCAATTACTTCTCATTTGAGTATTAGTAGACTGTCTTCTTAAAGGGCACCTATTTTACCCTTTTTTCAAGATTTAAGATAAATCTTTTGTGTCTCCAGAATGTGGCTGTAAAGTTTCAGTTCAAAACACTTATCAGCTTATTTATTATACCTTTCACAATATTGCACACAATGTAGCTGTTTTTGTGGCCTTTGCCTTTAATGCTAGTTCTCTCCGCCCACTGTTCCCACGTGTCACAGTGTGCCTCAATCTCTGCGTCAGCTGTGTCAGATAAACAGCACAGTGACAGACATGAAGACAGCAGATCTCACTTAACGTTTGTAAAAAAAAAAAAACTTTAGTATTGGACTTTCCCAATGATTATTTGATGTATTTGTTGTGGATTTAATTCTGCAACAATAACTGACAGACAATGTCATTACAAAGTTCACGCACACACATAAGCACGCATTTAACTTTTCACTGATTTTGCACGGCAAATGTGACAGGATACATGTTAATTTGATCAACCTCAACAGTCTACTTATAATCATGTGAGAATTAGTTGACATGTACAGTAGATGCAATGTAACTTAAACTCAACAAAATGAGTAAAGGGACCATCAAAATAAAATGATACCAAAAACTAATAATTTTTTAAGGAGGGAAATGATCCCTAATCATTTTTTCCTGTAATGAAAACATAAAATATATTTTTTTTAGAAATGTCTGGTTGCAAAAAGTTTTGCATTGGTCCCCCCTTAGAAATTTTTTATTTCTATTCAAAACCTGTATTGCTCTGAGAAACTATGTAAGTAAATGCAAGTCTTTGTGATAAAATACACAATATTGGAACTCAAAACATTTGCAACGAATTAAAACCATCTTACTTTTGGTAAACCTAACTGTTTTGTGAGTACATAAAAGAGTATTCCATCTCATTTGTCCCTTTAAGACCTTCAAGCAACATAGAAATAGCTATAATTTGTTATATTAGATGAACTTATATATTTTCTATAAGCCCTTCAGACATAATAGTGATGAATGGTGAAATTGATTAATGTTTAATTCTGAAACATTTTTAATATTTTACCATTTACAAAAAAATATAAGCTATTAATTATTCCCCATTTTGTGTTTGTAG
Seq C2 exon
ATATTAATGAGTGTGAACAGAGGGATACATGTCAGCACGAGTGTATGAACACTCCAGGCAGCCATAGGTGTTTGTGTCCCAGCGGCTATCGGCTTATGACCAACGGAAAAACCTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:104
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.123 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=32.8)
A:
NA
C2:
PF126622=cEGF=PU(83.3=48.8)
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:
GCTTGCCCAGCTATGAGACTT
R:
TTGGCAGGTTTTTCCGTTGGT
Band lengths:
350-2051
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]