RnoINT0071096 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67813501-67816771:-
Coord C1 exon
chr13:67816643-67816771
Coord A exon
chr13:67813852-67816642
Coord C2 exon
chr13:67813501-67813851
Length
2791 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GTATCATGGCACACGAGCAGACA
3' ss Score
-1.52
Exon sequences
Seq C1 exon
ACATTGATGAGTGCAAAGATGGGACCCACCAATGCAGATATAACCAAATATGTGAGAACACGAGAGGCAGCTACCGGTGTGCATGCCCAAGGGGTTATCGGTCTCAAGGAGTTGGAAGACCCTGCGTTG
Seq A exon
GTAAGTTACCAGAAACACTGTTAAAGTAGCTGATAGAGTTCCCTAACCTTACCAGAAGCTTGTGGTCATGCTCTCCTGCTACATGTAGAAGATAGATAAGTCTATTAAGAAAGTCATAATACAGTCTGCTTACTTACTACTATTAGATTTGACAATAAGTTCAATTTATATTGGCATTTCAAGAAATATTCTAGCCATTACCTGAGTGCCTCTTATATAATGCTTATATCAAAGTGAACTTCCAATATAACAGCCATGGCAGCTTGATCCTCATGACTACCTTATGATTTCTCTATGCACAGGACATAAACATCTGCATATGTACATTTTATTTCTTTGCGTATATGCATTAAATATATTTACATGTAGTATGAAATTTATGCATAAGAGTAAAACATGAATCCAATTTAAGTAAACATAATTATTGTATTGTCTACAGTGTTCAGTTCATTCAATTGCCTGGTTGTTTCCATCCTAGTTATGATGGACAATAAAGTAAGGCAGATGGTGGAGATTGTCTGTAAGAAGGGAAATCATGCTGGGGTGATACTCAGTGGGTAAGGGTACTTGTGTGGGCAACCTGGAGATCTGAGTTTGAATCCTCAGCACCCACATTAAAAAAAGAAGAAAAAGAAAGGGAAGAAAATTGTATTGTCTACAGTGTTCAGTTCATTCAATTGCCTGGTTGTTTCCATCCTAGTTATGATGGACAATAAAGTAAGGCAGATGGTGGAGATTGTCTGTAAGAAGGGAAATCATGCTGGGGTGATACTCAGTGGGTAAGGGTACTTGTGTGGGCAACCTGGAGATCTGAGTTTGAATCCTCAGCACCCACATTAAAAAAAGAAGAAAAAGAAAGGGAAGAAAACCAACTAGACATGACCATGTTTGCCTCTAACCATAGAACTAGGGAATGGAAACAGGTAGGTACTGGGGGTTCACTGGACAGCCTGCCGAGCCAAAATCATGAGCTTTAGACTTGTCAGGCAATAAGATGGAGTAATAGAAGAAGACACCTCTTAATTTGTTCTGGGTGATGTTCTCGGTTGTGGTAGGTTAACACTAAATAGTGTACGGCAGGCTTCTACCTTTAAGGTGTTTACCTCCCACAGGGAGCAAGGAACTCCCGGAATAAATGTGGGTACAACTTCAGGTCATGATAAACAATGTAATAAAATGAGATAAGGCCAGGGAAGGAATGAGGCAGGCCAGGATGAGAGGCACCTCTCTGGGGATTGGAGTGACAGGCTAGACAGTGTGAAGGTCTGAGCAAGTGCTTCAGGTCAAAACAGGCCCAAGTCCTGCAGACAGCAGCATACTGGCCACGGCTCAGAGATGGCCGCAAGACCTGGGCTGTCAGAGCACAGCAGGGCAGAAGATAAAGAGGCCAGGGGAAAATTCTTAGACCACCTTTAAACTGCAGTGAGAAGACAGGAGGGGTGTGGTGTGAGGCAATTCTCATCTGGAAATGAGCCCTCTTGCAGCCATGGAGGGAGTAAGTGATGGGGGCCATGATCTGGGTGGAAAGACAAAGCTCATGATATAAAAATAAATAAATATTAATTATGTGTAATAATAAAAAGTAAATAACATATTTATTTTTGATCTTTATGGATTCATAAAAACTAGACCTAAACATACTAGTGTTTCCCTCAGTGCCAAGCAACCAGGAAAGCCAGAAATACATCTGAAGGATCAGTTAGTCAAAAGAGAAAAAGAAAGGGACAGAGAGATGGCTCAGCAGTTAAGAGCACTCATTCCCCTTCTAGAGGACCCAAGTTCAGTTTCCATCACCCACATCAAGCCACTTGCAAATGCCTGCAACTCCAGCTCCAGGGGCCCAGCACCCTCTCTTGGCTTCTGAGGGCACCCAGAAACACAAGTGTACACAAGTAAAATTAAGAGTAAAGTAAAATAAATCTTTTTAAAAAGAGAAAATTGTTAAAGTATGCATATATCATTTTATTAGAAGAGACAAATATTTAAATAATTTTTATTCCACTAAAATTACACTAGTTTGGGGGCTGGAGAGATGGCTTGGTGATTAAGAGCACTGGATGCTCTTCCAGAGGACCCAGAGCAGCTCACAACTGTCTGTAACTCCAGTTCTAAGGGATCCTACACCCCCATACAGGCAAAATTCCAATGCACATATAATAAAAATAAATCATTTTTTAAAAAATTACACTAATTTGGATTCTATACCTTCTGCACCTTTACTCTCCAAAGAAGGTGAAACATTTCTAATAATGTAGTAAATCCCTACCTACTTTAGGAAAAGTAGTATTTGGAAAGCTGAGTATATGTGAGTTATAATATTTCCTTAATTAAATCCATTACTGTATATGCTAGCGTAAAATAAGATTAAATATGTAAATGGAAATCTTGTTAAAATGTAAAATGTAAAAATGTGCGTCAGCTTACCCCAACCAGATACACATCCAAGCTTGGTTTTGCTTTGAAGTCAAGGGGACAAGGCTGAAGCATCCCACCAGGCCTCAAGTCCATAACAGGAAAGCAAAGAGCAGATGGATTCCCAGAACTAGTTAGTGTCTTGCTTCCTGGGCCACCTGCTGAAGTGTGAACGTTTAAATGAAACAAATGCAGATGGAGCAGTGCTCAGAAAGGGGCACAGTGTCTCCAGAACTGAGTGGGTCAAGCTTTGGCATCAGCGTCGGAGAGTAATACGATGTCTTGACTTGGTTTCAGCAACTGACTGTTTATCCCTGTTTTGTGTGTGTCTATTTTTTCTCTCCCCCTCTCTCTTTTATGTATCATGGCACACGAGCAG
Seq C2 exon
ACATTAATGAATGTGACCAAGTACCTAAACCTTGTGCACATCAGTGCTCCAACAGCCCCGGCAGCTTCAAGTGTATCTGTCTGCCAGGACAACATTTATTAGGGGATGGGAAATCTTGCGCTGGATTGGAGAGGCTGTCGAGTTATGGCACTCAGTACAGTAGCTATGACCTTGAGCGGTTCTCCCCTGTGAGAAGTGGCTATCAACCTCGGCAGCATACCAGACAGCAGTCACAGCTCTACAGCTCCTACTCAGAGTATAGGAACAGCAGAGCATCTTTCTCCAGGAGTAGAAGGACTATTAGGAAAACTTGCCCTGAAGGCTCTGAGGCAAACCATGAAACATGTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:104
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=0.157
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=33.9)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]