DreINT0078203 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34323985-34327650:-
Coord C1 exon
chr20:34327555-34327650
Coord A exon
chr20:34324113-34327554
Coord C2 exon
chr20:34323985-34324112
Length
3442 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
TCTGTATTTTTTGTGTGCAGTGT
3' ss Score
7.95
Exon sequences
Seq C1 exon
ACCTCTGGGTTGAGGATGAGGCCACCTATGTGTGTGAAGCTCAAAACCACTTTGGCAGAATACAGGTCAAGGCCAAAGTCACTGTGACAGGACTTG
Seq A exon
GTATGTCATCTGCAAAAACAAAAAACAAATCCTCTTCAGTGATAACTGCAACATATGTTTCATGTTTATGCTGATCCCTCTGTCAGCAGCACACTTGAAGAAAGAAGCTGGTGTGGGATATGAATTGTTTTCCACTTCCTTAATCATGTACATTTTCTCGGCCTGAGGCCCGTAAGCTTAAGTTCATGAGGTCCTCAGCAGCTCAGTTTGATGTTAGAGTCCATATGAATTTATAAGGCTACAGGGGTACATGTGGTTCTAGTTAAGAGAGATAGGATGCTATAATAAGAGACCAACACCAGAGTTAGCGCAAATTCATTCTTCATGGCGAGCGATACCGCACCAGATGTGAGCACTGACACATCCATAATGCATTGCAGTTTTGTTTACTTTAGTTATTAGATGCATAGTGTGTATTTGTGGTTGTTTAATAACATTGTATATTTATGGTTGCTATTTTTATTTGCACATGTGAGATTAAACTAATGTGTACATGCATGCCTTGGGAGCATGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCAGCTTTGTCTTCAGAGAATGAAAGGAATTCAAACATGCTTTCCTACTTTTTTCTTTAAAGAACCAGCAGTCTGTTTCTGGCATCTGTAAAGTTGAACTTTATGAATTTTGATCTTACAGGATGACATCTATTAGTTAAGACATCACCCTTTTGGCCTGCTAGACACTTTAATACATTACCGCAAAAAAGGATTCTATTTATATCCATGAGGACAAAATCAAGTCTCAGCCCCCATTTTGTTCTTATTCAACAAAAGCATTTTGATACATATCACCATAGGAAAAAAAGATGACTCGAAATGTATACTGTTATGATGAGGCAAAAGGGGGCACATTTTTGTTATCCAGATTCATAAATACACTAAAGGCTTCTAAAAATAAGTATCATGCCAAAACCTCAGCAAGGGTCAATTGGATGTGTCATTTTGGAGTGCACACTGTGTGCAAGATCAGAAGTGTCTCCAGTGTGAGTGTATCTCTGTGTGAGAGGGAGTCACTGAATTTTTGTGGTCCTATAAAAACAACACAAGCTAAAGGTCACTAATGCAGTCTCGGAGTGCATCTCAGCAATCCCATAATTCTGCTCAGCTGAGCCCTAATAACTCAGTGACACTCTGTATGTGTATTCCAAGGTATCCATGGAAATGTAACAAGCAAAACAGCAGAGGTGTGGTCAGTCCATTGAGCTTGTAATGTCAGTGTTTCCAGTGGAAGCTGTTTTTGAGAACGTCCTAAGATTGAATTAAAAGAATCTAAAATGATCAGGATCATTATTTGAAAGTCTTTTCTACTTAAAAAAAATTAAATGTTCATACAATCGTAATATCTCAAGGTTTGATGTGAAATTCATTATTCCTTTAGTCCTTGTGGTATGCGAAATAGGTAAAATTTTATATGTAAAGTTGAAACCAGAAGTTTACATACACTGTATCAAAAGGCACATAACCTTTTTTCTTTTAGATGTTAAATGTGATTAAACTTTTTCTTTTTTAGATAAGTTAAAATTACCAAAATTGTTTCTATTTGCTTAATACCAGAATAATGAGAGAGAGATTTTTTATATTACTTTCTTGAAAGTCAAATGTTTACATACTTTAAGATGTAGTATGCCTCTAAGAATGCTGATGATGGTGTCAAGAATTTGGAAATTCTGATTGGCTAATTGACAAGATTTGAGTTACCAAGAGGCACACCTGTGGATTAGTATTTAAGGCAAACCTCAAACACACTGCTTCCTTGTATGACAACATGCGGAAATCTGAAGAAATCAACCAAGACATCAGGAAGAGAATTGTGGACCTCCACAAGTCCAGTTCTTCTTTGGATACAATTTCCAGATGCCCGAAGGTGCCACATTCATCAGTTCACACAATTAAATGCAAGTATAAACAACATGGGAATGGCCAGCCGTCATACCGCTCTGGAAGGAGAATAATTCTGTGCCCCAGAGATGAACGTGCTATGGTGCGAACTGTGTGAATCAAACCCAGAACAAAACCAAAATACCTTGTGAATATCCTGGCTGTAGCCGGTAAGTTTCATTATCCACAGTGAAATTAATCCTGTACTGATATGGGCAGAAAGGCCACTTAGCATGGAAGAAGCCATTACTTCAAAAGCAGCATAAAAAGTCAGATTACAATTTGCAAAATCACACTGGGAAAAATACTTGTGCTGTATGTCCTGTGGTCTGATGAAACTAAGATTGAACAGTTTTGGCCATAATGACCAGCGTTACATTTGGAGAAAAAAGGGGAAGCTTATAAGCCTGGGATCACCATCCCAGCTGTGAAGTATGGGGGCGACAGCATCATGTTGTGTGGCTGTTTTGCTGCAGGAGAGACTGGTGCACTTCACAAAATAGACGGCATCAAAGGAAAGAACATTATCTAGAAATGTTGATTCAACATCCTCAGCCAGAAAATTAAAGCTTGGCTGCAAATGGGTTTTCCAAATGGACAGTGATTCTAAGCATATGCCAAATTAGTTTAAACGTGGCTTAAGCACAACAGAGTAAATGTTTTGGGGTGGCTATCACAAAGCCCTGTTCTCAACCCTATAGAAAATTTGTGGGCAGAGCTACAAAAACGTGCGCGAACAAGGCAATCTACAAATCTGACACCAGTTCTGTCAGAAGGAATGGGCCAAAATTCTAGCAAACTATTGTGAGAAGCTTGTGGTAGGATACCCAAAAATTTTGACTCAAGTTATACAGTTTAAAAGCAATGCTACAAAATACTAAAGAAATGTATGTAAACTTTTGACTGCCTAGAAAGTAATAAAAAATTCTCAATATTAAATTCTCTCATTATCCTGCCGTTTAGCAAATATAAATCTAAATGGTTATGTGCCTTTTTATAGAGTTAAAATGTCTTTTATAAAGTGTTTTCATATAATGTGCCATTGAAAGGCTTGGAGTCTTAAAGATTTTTTTAATCTCTCCTTACCAAGTATGCATTTATTAGATAAAAACAACTGTCAAGACAGCCTTTGCGTAGAAATCATTTATTGACTAAGGATAGCCACATTTGCATATTTGCATATATATAAACAGGTCAGTGTCACAAATTTTGCTCAAGCATTTAAATAAAAAAATATATATACTGTATATTTAAAATCAGGATTCAAACTTCAAAACAAAAGCATATATTGTAAATAAATTGACAGAGACTTTCAATCAAGTAATGCTCCTTGGTTTAATTAATTTATAAACTTCCTTAAAACTCTAACTGACCAAACTTTCCAACAGTATCTTCATAAAGCTTTCTATATATGCTAATATCTGTATTTTTTGTGTGCAG
Seq C2 exon
TGTCCCCTTTAATAGCTCTGAGTCCCACAGTGGTCAGTGTAATCGAGGACCAGCAGGTCACTCTTCCCTGTGTGTTACTTGCTGGAAATCCTCTTCCTGAGAGACACTGGCTGCACGACAATGGCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:17
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=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(30.4=84.8)
A:
NA
C2:
PF0767911=I-set=PU(45.5=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]