RnoINT0071099 @ rn6
Intron Retention
Gene
ENSRNOG00000028627 | Hmcn1
Description
hemicentin 1 [Source:RGD Symbol;Acc:1564772]
Coordinates
chr13:67799791-67802816:-
Coord C1 exon
chr13:67802690-67802816
Coord A exon
chr13:67801178-67802689
Coord C2 exon
chr13:67799791-67801177
Length
1512 bp
Sequences
Splice sites
5' ss Seq
GGGGTATGT
5' ss Score
7.48
3' ss Seq
CATTTATTATTTAACCTTAGGTT
3' ss Score
8.36
Exon sequences
Seq C1 exon
ATGTCGATGAGTGCTTGGAGCAGAATGTACGCTGTGGGCCGAATCGCATGTGTTTCAACATGAGAGGAAGCTATCAGTGCATCGACACACCCTGTCCACCCAACTACCAACGAGATCCTGTTTTGGG
Seq A exon
GTATGTTTCTCCTTCTTCTCCCAGACATGCTTCTGGAAACCCTGCCTTTGACCAACATAACCTTATTAACAGTCATGCCTAACTCATAGAACGTCAGTAGCCCTGGGGGGATACGTGCTGATCATGTGTTCCTTCTTCTATGAATGGACAAGAGATAAACTCATTAGGCAGCTGCCACTGTCAACCAAACCATCACTCATGATTGCCAAGCCTTCCTGGATGAGGCTTCCATTATGGAGTCCAAAGCGTAGCATCCAGGGCTCTCCTACACAGCAAGTGTTCTATGGGATACAGAGCCAACCTTTCTTTCTTTAAAAGTTCCTCATTTCTATTTGTACTGTCTCAAGCTGATAAGTCTTGTAAGCAGGTAGACTGAAGTCCCTCTTCTGTTGCTGTGGTGACTCACCATGCATCCAGAGAAGGAGAGAAAGAAGGATGAGTCAATAGTCTGACCATAGGTGGTGTCTTGCTCACATTTCCTGGTGCCTGACAGTCTTCTTGCTTCTGGAAAAACTATTCTAGTTTTTCCCACCCTGTCTAGGTACCAAGGATTCTGGATGTTTGAAAACAAGTGATAATGTTTATCTTTGGTGTCCCTGTTCATCACCAACTGCTCACTGGACTCACACTTTATTTTCCTCTTGGTAATGCCTCCTTAATGTAGCATGGTCGAGTGTGTATTGTCAAGGACCTACCATAAACCTGCTTGTGATGAATCTTGTAAGGATGGAAACAGGAAGAGGGATTTAAATTATGGAGACTTATAAAGTATCTAAAAATGATTTGACTAAAGAATCTATATTTTCATAAAATAGTCCTTTGCGGAGTTTTTTTCCCCCATCTAGATCTCTAGAAAAAATAATTTAACTGTCATTATGATTTAGTGTGGGCTCTGAGAGTGGGAAATCCTTTTAAATGTAAAATAATATAAAGAAAAGTTTAAAAGGAAGTCATCCCCTAGAAATCCCAAGTAGCCTTTATTCTGAAAAGAATAAACGAAATAGCTGTATAGCCTATGTTAACCTTCAACCAGCATTAGGATGTTCTAATGTCGCTTATTGTCCTCTTTCTGGGAAGTATTATTTTCCAAGATACATATGATGCATTTGTTTCTGAAACTGACTTTTTCATTTTAACAACAGCTCTCTTAGGAGTGTTCAGGAGCTGTGAAGCACAAGGCCAGCATCCAATGCTAGCACCCCACCAAAAGAGAAATAAAGCATTAATGTATTCTTGCTTACTTCAGGAACTCCAATCTTCTGATTTTAGTAGAGCAAGAATATTGATACTTGACTGTAGACCAGTTTTTGGTTTTGTTTGTTTGTTGTTTGTTTGTTTGTTTGTTTTGCTTCCCGGTATCTCTTTTGAGCCAGTGATTTAGGACATGGGGAGAGCCACATTTGTAGGTTAACAAATGACTAAGAGTCACCGTGGGTCATGATCACTTGTATTGTAGCCTATCTTGTTCCAGGGTGTGTAACTCTGTGCATCTCATTTATTATTTAACCTTAG
Seq C2 exon
GTTCTGCCTCAAGAACTGCCCACCCAATGACTTGGAATGCACCTTGAGCCCCTATGCCTTGGAATATAAACTTGTCTCCCTCCCATTTGGAATAGCTGCCAATCAAGATTTAATCCGGCTGGTTGCATACACACAGGATGGAGTGATGCATCCCAGGACAACTTTCCTCATGGTAGATGAGGAACCAGCTGTCCCTTTTGCCTTAAGGGATGAAAACCTGAAAGGAGTCGTGTACACTACACGTCCACTACGAGAGGCAGAGACCTACCGCATGAAGGTGCGGGCTTTATCCTACAGTGCCAACGGGACCATTGAGTATCAGACTACATTCATAGTTTATATAGCTGTGTCTGCCTATCCATACTAGGAAGTACTCCAGAATTGAGTCCAAATATTTAAACTGCATTGATCTAGCAATCAAGGACCTCTACAATTTACTATCTCTTGAACAGTTGCAATCTTGGCAACTTGAAAATGGTGCTGTGCTGTTATGTATGTGTTCCTTGGTACTGCTGAAGTATCTGTATGATCCCACTGTGGTCATGTATCTTTTAGTACGTTCTAGAAGAGTCCTTTCTTATTGTCTTTATTTATTACACTGGAGCAGTTACTTCCCAAGGATTATTCTGATCAGCTCACAGGACATGTCAGTGATATTGTATAGTAGCATAGTAGCTAAGATCATTTTCTTGGAAACAATATAGAACAAAACAAAACAAAAAACTAGTTCAAATACTTTTTGAACATTTTGGCTATTCTTAAAATGGTAAAAACCAGCTATTATGTGTTTTGATAAAAGCTTATGCCATATTATACATTTTTAAAATATTGAAATAACACTTATATCTTTCATTTTAAGGTTAAAAATAAGAAACATCACTTTTCTGAAATATAGTGCAGATACAAGAAAGTTTGCTTGATCCGAAATGGATCTTATCTTTATTAAATACTCAAGATACATTACCTGAGGTTCTGCGAAATCATGTGAACTTTGTACTATGTTATCAGAAAATTACTTTCCCTTTAAAGAATTGCCCATGGCCTAGGCCTTTGACATTTTGGTATTCACTCAGCTCCATAACTTTTACATTCCATATCTATCTGTCAAATAAAATTATTTTAATACATAACAATAGAACAGATTTCTTGATTATTGTACTCATGTATGTTCAAGTAACGTGTTAAACGTCAATACACTGTACATGGTGGTAACAGACTCTGTAAGCAATTGTCAAGATGTATTCTATTTTTATGAAGTGTATATATTACCTTAGTGTGTATTTTCTATATAATATCTTGATGGACTCTTTTATAAAATTATTTTATAAAAAAATTACAGTAAAATAAGCCTAAATAAAATTTTCACCTTTTTCTTAATAACCTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028627:ENSRNOT00000030971:107
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(16.7=9.3),PF129472=EGF_3=WD(100=81.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTCCACCCAACTACCAACG
R:
TCCCGTTGGCACTGTAGGATA
Band lengths:
344-1856
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]