RnoINT0071097 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67809640-67813851:-
Coord C1 exon
chr13:67813501-67813851
Coord A exon
chr13:67809760-67813500
Coord C2 exon
chr13:67809640-67809759
Length
3741 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAT
5' ss Score
6.62
3' ss Seq
TCTGTTTTCTTTCTAAACAGATA
3' ss Score
11.55
Exon sequences
Seq C1 exon
ACATTAATGAATGTGACCAAGTACCTAAACCTTGTGCACATCAGTGCTCCAACAGCCCCGGCAGCTTCAAGTGTATCTGTCTGCCAGGACAACATTTATTAGGGGATGGGAAATCTTGCGCTGGATTGGAGAGGCTGTCGAGTTATGGCACTCAGTACAGTAGCTATGACCTTGAGCGGTTCTCCCCTGTGAGAAGTGGCTATCAACCTCGGCAGCATACCAGACAGCAGTCACAGCTCTACAGCTCCTACTCAGAGTATAGGAACAGCAGAGCATCTTTCTCCAGGAGTAGAAGGACTATTAGGAAAACTTGCCCTGAAGGCTCTGAGGCAAACCATGAAACATGTGTAG
Seq A exon
GTAAATGTCGGCCATATTGCATTTCCTTTCTGTGAGCTCACTTCTTGTCCGGAGTACTAAGCCTTTATACAGCACCTGTGTTTGGTGCACCGAACCACCTCTGATCTCCAGGCTGGACTGACTCAAAGGGTTTTTTGGGTTTTTTTTTTTGACATTTATTCTGGCACCTAGGGTGATGACAGATTATCCAGATAAATGATGTATTTGCATGTGTGCATTCTAATAATGTTACATTGTTTCTCTTTCTGGGACCTGTTACTGAATTAAATCCTACATAGATATAAAGGTCAGTGCTATCCATGAGGTGAGTTTTTTTAGAGAGATACACACATTGTTGCATAGTATGTATGGTGCAAAAGCTGGGGCTTAGAAATGAGAGTTTTGACCCAGTCAGCTGTTCTTTGTAACAGCCCACATTCTGTCAGCCATTGTCCCCAGTCTTCCCATGAAATTGTCCAGTCAGGTTATTTTGTATGTTTATGGCTAAAGATAATGCGATCCAGAGCAACTTGGACCCATTGCTTCAAAATATGTGTGCTCGGTATCTTTATCTAAACTCATAAGCCAGGAACTTAATTTACAAAACTTATCTATAATTTCCCACCAAAGACTCTAGTCCTTATTTTCAGCTAAGTTGTAAACATTGCCATCTGCCATAGATTTAACTCAGTTTTGGTCGATGTCTACAGTTTGCCTGTCGTCGAGCTAGACAAAAAGAGGAATTAGCAAACGACAGTTAGCCCCACTATTTTGTTAGATGGCAAAAGGAAGCAAACAGGAAAGGAGGAAGGCAAGAAAGAACTCTTATTCAAAGGCCATTGGACTGGACCATTCATCCATCCTTAAAGCTCTCTTCAAAGACCATTGGAACATCTCATTCTAACAGTGTCTAACATGTTGTTCATACTAAGTGATATATTCTCTCTCTTTAAGCTGTTTTAGTGTCTTGAGGTTTTCTGTATCCTCTGACTTGATAGTTTTCATTTACTTTCTGACTCGTCCCCATCCTGTTACCTTTTCTGATGCACGTGCCCAGCCAACTGTACCTGGAGCCAGATCCTCCTATCGTACAGTCTTAGCTGTGTCCACCGGACTTCCTGAAAATTTGAACTTTATACCTTATTATTGCATTCTTATTGATCCAATACTTTTCTTTCTATTTATCCCAGGGTAGCTAATGTGTATCATTATGGATATGTTAACTTTGCTGTGTAATGGGCTCTCCAGAACTACAGACACTGTCAAAGTCTTACGCTTTAAACTTCATGCATTTATTAGCAGGGCCCTGCCTTTGGTCGAGTGTGGACAAATAACACATGGTCACTGCTTCTCTGCATCTCCTGTCACTCTGAGTGATTGACAGCTTTCAATGCCTACAGTTTTGATCTGGCTCTTTGCTTACCTAAATGTTCATGATTCGTTTAGTAATATGTTGTCTTTAAAAGTGTCTTCTGAGTAGTTACTCTGACTACGGAGGGCTTTGTAGCCTGCCATCCTCCCACTTTTGGCTTCATTTTGGACAAACTCATTACTTCTAGCCTTCTTTTATTCTTTTTACCTCAAAGTCATTGCTCGTGCCCATGCTATAACTGAACTAAACCACGCGCTCACACCGGGCATCGCCTGACTGCTGCCCTCTAACGACTGAAGCTGCACACAGCTTTAGAAAGATCCTCTTACCAACAACCCAACTCCCTGCCTTCATCATTGCTTAGGGCTGCAGCTCCACCACGCTAGAGTCTAATGGAGCTTTGCTCTCTTGATGTCTACCATACACCAATACTGTGGTGCATCAAAATTACCTTCTTCCATAGGCATGCATTGTTCAAGACTATTTTACAGTGAGTATCGATCCTGTAAAACCTAAAGTCAGCATTTATAACTCACTGACCTGTGGCCTTCCCATTTATTGGTGAAACAGTGAGGAGTCTTACATATTTCTTAAAATACGGTGAATATTTTATTGGGGCTAATGAAGTTATTCACGCGAAGGTTGCAGACAGTTCTGGAATCGTCAAACAAAAGCAACTTACAACAAACACTGACTGCCTTTAATTAACCATCTGGGGCAGACGCGTTACAAAAGGATTAAATTGACATTGTGGAATCTTGTTAGATTTGGGCAGATTTTTAGTTTTTAAAGAGTCAATCCCAGGGTTTAACAGAAATAATGAACTTTGCTCCGGTTCTGAGAGCAGAAATCACACATTGCCATTTTAAAATTCATATGCTTGGAAGCTCCATGTTAATGACTTCGAGTTCAAAAATCATTTGAATTTCTGTTGTTGTTTTAGATTAAAGCAAATATTTAAAGAGAAAAGACAAAAATAACTCATGCAAATTATGAGATGAGTACTTTGGCTAGCTAAAACGGTGCATAAACATGGGAAGTGAATATTTGCTGGATATTGTCATTAACAGGTTTTGAATCGTTACAATTATGTTTTCAGCATGTGCTGAGCAGATTCATTAGCTGAGTCATCCACCAGACTCACTGTGTCTTCGCTTCATTCTACCCTTCCTCCTCCTGTTCCCCTTCATGGCATATTCCTTGGTGTCCCACTGGTTAGTGTATTCTCAGTGACCATTAGAGATTTGATTAAAAAAAAAAAAAAAAGACCATCAGAATCCAAAAGCAAAAATCGAGTTTGAATTATCATCTAGTCTCACTGTACTTTACTGTGTATGATTTTTTTTCATATTAATGATAGTAGGCAGCCTCCCCACCCCACCCCCTCTGTGGTTTATAAAGTGTTTTCTCACTTACTGCAGTGTATGGATCTCCCAACAAACCCATGAAGTGGAATAGATGGTTTCCATGCTCCCTTTTAGCAGAAGAATTGACTGAGATCTTGAGAAATTAGATGAGTTCCCCAACTTAGCACAGCTATAGACATGTATCTGCCACTAGTAGTTTGATATAAAAGATTGAGAAATATTTCTCACAAATATGGGAACGCTTTCACTTGAAAATATCTGCATATGTGAAAGCTTTGTATAGATATTGTAGGGGGGAAGAGAAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGTATCGAAGTTCACATGAAATAAAACTGAGGACTAAAGAGATGGTTCAGTAGTTACTCACACTGGCTGCTTCTCCAAAGGAGCTGTGTTTAATTCCCAGCACCCACACAGTCTGTAACCCCTGTTTCAAGGGACTCAATGCCCTCTTCTGTGCATATGCACTGCACAGCCATGGTATACAAAGGCAAAATACTCATGGACACAAAATAATAAAATAAAAGTTTTTAAAACAGATACCTCCTTTCCCAATTAATAGCAAAAGAAATTTCCAGGTAAACTTTACCATTTTATCAAAATGTTAGCTTTTTTTTTTTGTGGTTTCAGATCTTATGCAGAGCTGCCCCCCCCCAGTCATTTTAATGTAATTTAGCAACACAGGAAAAAAATGGCAAAGTTGAGACTTCAGGTCATAGATATTCATGTAAAATAATAGAGAAATGCCCGTATATTAAAAAGTAGTATAGTGCATCTTATAATACAGTTAGTATTTATGTTGCTAAAAACAGGCTTGGTGTATAATAGCTCTAAACACTTCTAAGAGCATGAATGTGAAGCCACCATGAATGTTTCTATGTTATGCCCGCCACGTATATTGATAGCAGTGTCACGGATCCTGCTCACATGACTGTCCCTTTGGCATGACTATGTACTCTGTTTTCTTTCTAAACAG
Seq C2 exon
ATATTGATGAATGTCAAAACAGAGATACTTGCCAACATGAGTGTAAAAACACGATCGGAAGCTACCAGTGCGTCTGCCCACCGGGTTATCGACTCATGCTCAATGGGAAAACATGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:105
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.157 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=33.9)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
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]