DreINT0078196 @ danRer10
Intron Retention
Gene
ENSDARG00000016936 | hmcn1
Description
hemicentin 1 [Source:ZFIN;Acc:ZDB-GENE-041014-322]
Coordinates
chr20:34254429-34256328:-
Coord C1 exon
chr20:34256202-34256328
Coord A exon
chr20:34256120-34256201
Coord C2 exon
chr20:34254429-34256119
Length
82 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGA
5' ss Score
6.65
3' ss Seq
AGATCTCAACTTCGTTGTAGGTT
3' ss Score
5.52
Exon sequences
Seq C1 exon
ACATAGATGAATGCCTAGAGCAGAACATTCAGTGTGGTGCAAACAGGATGTGTTTCAACATGAGAGGGAGTTACCAGTGTATCGACACACCTTGCCCACCCAATTATCAGAGAGATCCTGCCACAGG
Seq A exon
GTGAGACGGACACTCCATTCTTTCAAATTGCCTACTTTTAGTTAGCTGATTGTTCAAAATCAAGATCTCAACTTCGTTGTAG
Seq C2 exon
GTTCTGCTTGAAGAATTGCCCGCCTAATGACCTGGAGTGTGCCCTGAGCCCATATGCACTGGAGTACAAGCTGCTGTCCTTGCCCTTCGGCATCGCCGCCAATCAGGACCTGATCCGATTGGTTGCCTACACCCAGGATGGAGTCGTCCACCCGCGCACTTCCTTTTTAGTGGTCGACGAAGACACGACTCTGCCCTTCGCCCTCCGGGATGAAAACCTCAAAGGTGTTCTGTTCACCACCCGGCCACTGCGCGAGCCTCACACATACCGCATGAAAGTGCGAGCTCTGTCTTACAGCGCCGACGGAGGAATAGAGTACCAGACCACCTTCATCGTCTACATCGCTGTCTCAGCCTATCCCTACTGAGCACTTTATTACGCCCACAGCCTAAGAAGAGAGGGACTGCTCAGAGGTTGCGCTATGAATCCATCATTTAATGGTTTACGAACACTTTCAGACATGTTAATGGTGGTGTCCTAAAAGTCAAACTAAAAAATTCAACTACATCTGTTAATATGAACCAGGAAAGAGATGCAAGAGATGATTTGGATAGAAAAACAACAGATTGCAAATGTATGCTAGCGGAATCATGTTGATCATTAAATCATGTGACTAGTTTGTGTGTATCTTTCACATTATGAACAGTAAAGGCCAAAAAAGTAAGACTTAAAGCCCTAAACTTTAGCGTGACCGTCCATTTAATTTCCAATGTGATTTTCAGGAGGGTCAGTGGATGGATTTTGTGTCCCAGCAGACAGTATGCATACATCAGCAATGCACAAAGGGAATATTGAGGTGGAAGAATGCACGTCGAACTTGTTTATCCACTGCTGGCTATACATTGAAACCTACATCACAAGAATGCAATTATGATAAAGATGCAGTAAAAATGCAAACTTAAGTAAACACAAAATGAAAAAGTTTGTATTGCTGAAATATCAAAACAGAGAATGTTGGAAAACTTTCAACATAGTCCATCCGGATACAACCTTATATAGCGCAACCTCTGAGAAAAGTGCAGTTTTTGTACATGCATGACTGAGAAGTGTGTCCTGAGAGTGTGTGTTTGAGTGCTGATCCGCCACTTGAAGATAATGTCTTTTAAGGCCTAGGAATTATCAGCATCTTGCAGATAAACATAGCTGTTCTCACTGGAGAGCTCAATCCAGACAGACTTCACGTGAAAGCAGTTGTAAGCCCGCAGGTTAACAGATACATACAAGAACCCTCCATCTGAATGTGCATCAGGACAGTGGGTGGTGTTCTAAAATACGACTGCATTTACGTCTACCTATTAACTTATTGGGAATTGCTTGAATATATGGAAGAGACTCAATTCCCTCCATTGCTTTCTATGAAATGAGATGAGGAAGATGTGTTGCTTTTAATTTGTGCTTTGCAACATGATGATGAGGTTTGAGCCACATGACATGACAAGAACGTCCACCTCAGGTAAGCACTACCTTTACTCCAAATGTGTTTTGACAATCAGTAGTTATGCAGATAATAGCAATGTCTCATTAGCATCACAGGTTCATACGCATTTGATCTGTTGTTTTGTGTTTTACTTTGTTCAGTAATCAAGGTGTATTCTATTTTCATGATATGTATATAAGCATTTGGGTTTTATTTGTAATATGATGTTGTAATCCCTTTTTTAAAAAAAGCAATAAAATGTACAATACGTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000016936:ENSDART00000144705:106
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(12.5=7.0),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:
TGTGGTGCAAACAGGATGTGT
R:
GCAGCTTGTACTCCAGTGCAT
Band lengths:
169-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]