DreINT0078291 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34263792-34265718:-
Coord C1 exon
chr20:34265481-34265718
Coord A exon
chr20:34263855-34265480
Coord C2 exon
chr20:34263792-34263854
Length
1626 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
ACATTTTTTTTTTTCCTCAGGAG
3' ss Score
10.49
Exon sequences
Seq C1 exon
GACTACACTGAAGACTACATCCAGACAGGTCCCGGACAGCTGTATGCTCTGTCTACACGTATGTTCAGTATAGATAGGGTGAGTGTGCCTTACTCCTGGAATCATACTATCACATATGGACCATCCAGGGGAAAGATGCCGTATTTGGTGCAGACGCTGCACGCCTCAGCTATCAACGCTTTGTATCATCCACTAGAAGAGATGCTGGAGTTTGCCATCCAGGCCACCATTGCTAAAG
Seq A exon
GTATGGTACACAAATAAAATTCCTTTTTTTAATTGTTTCATCATTGTTAATATACATTTCTATAAGTATCTTTTTATTAACAGACAGTGCAGGCTTTTTAATGGATTCGACTTGTATAGGAATAGTAGGCTATAGTGATGGGAAGTTCAAATGATTTTACTGACTCTGACCATTAAGTCCTGTTCAGCAAGGTGAATGAATCTTTTTTTCGAGTCATTTCATTCAATTTGCTTAAAGCAGTGGTTCTCAAACTATTTTCATCAAGTACCACCTCAGAAAAAAAATTGTCTCTCCAAGTACCACCAAAATAAGCAGTATTAAAATACAGTAGCGTAGTAGGCCCAGTAAAGCAGCTACAACTCTGCACAGTTAAAAAACGTGACAGATTACCTCATAAATTTAGGCTTTATGTCATATATGACATATTATATACATCATATTTAATAAATTTATGTAGCATGTACATGACATATTTAATTCCTCCGTGTACCACTAGTGGTACATGTACCACAGTTTGAGAACCACTGGCCTAAAGTATTATTAAAATGTTGCTTTCAAACTCATTTACAACTACACCAAACATTGCTACACTACAAACAAGTCATAGCTAGAATGCTGTAAGAAAGAGAAAATAATCATTGATTGTTTTCCTGGTCTTTTGTCTATGATTATATCAGCTCACCTCTTGTGACAGGTCTTTAAATCAAGTCCCATTTAAAGCTTAACTAATGGACAAAGTCTGAGCTGTAAGGAGCCATGATTAGTTCATCTTTTGAATCCTCTGGTTTTTGAGTCTTTCGTTCATCACGCATGTAAAGAGAGATGACTCAAACACGAGGACTCGAGTAATGACGAATCAAATCTTATTCAGACTGTAAATGCATATGATTGGCTTCTATCTTTCACATGAGGAACAAACGACTCAAACCGAGGACTCGAGAAATGAACGAGTCAAATCTGTTTTTCCGCCTCTAACTACATATGATTGGCTTTTGCCTTTTATGTGATGAAAAACAACTTAAACCTGATAAAAGACTTGAAAAAGGAATTAATCTTATACTCGCAAAGGAATAATTCACTTCCTGAGAGGACTCATCATTCTCAAGTCATAATGAGTCAAAATGGCAAAATGAATGAAATGGTCAAGAACGACCCATCACTAGTAGGCTAGTATTGGTAGTAGCAGGTATTAAAAACCTCTTTCACACATACAGACTTTTCTGGAAAATTATGGGGAAATTGCCATGAAGGGATCACATGTGAACAGGCCCTTTTTAAATTCTGGATTATGTGTTCCTATTTTTTATTTTTTTTTGGAATTAGATGTAACATTACCAGTAAATTACCATAATTCTGCTGGTAGAATTAATGGAAAAAACGTTCTGGTTATTTTACTGCAGTTTTTAGGTGCCATATTTTTAAAAATACTAATCTGTTTTCCAATTTTTTGTGCAAAAAAGCTGCAAAAATTGTATACTATTACATTCCCAAAAATCAAAAAAAACTCTCATATTTGTATGCTTTAGCTCTTTATTAATTTCAGATCATTTTATTTTTGTGTTTGATCTTTTTAATGAGTAATAATGAGTATCCTTCTCCAGTTACAACATTTTTTTTTTTCCTCAG
Seq C2 exon
GAGAGCGAAGTAATCAGTGTCCCAGTGGTTTTCAGCTGGACCCTACTGGCCCATACTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:97
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:
PF074747=G2F=PD(26.2=61.2)
A:
NA
C2:
PF146701=FXa_inhibition=PU(4.9=9.1)
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:
ACACTGAAGACTACATCCAGACA
R:
AACAGTATGGGCCAGTAGGGT
Band lengths:
294-1920
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]