GgaINT0000517 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:358992-359887:+
Coord C1 exon
chr8_random:358992-359252
Coord A exon
chr8_random:359253-359713
Coord C2 exon
chr8_random:359714-359887
Length
461 bp
Sequences
Splice sites
5' ss Seq
AGGGTAGGT
5' ss Score
8.1
3' ss Seq
GAGTACCATTTTTCCCACTGCAG
3' ss Score
-2.11
Exon sequences
Seq C1 exon
TCATCACCATTGAGCCTGCAGGGACCACTGTTGAAGCTGGTGCTACAGTAATGCTGAACTGCCAGGCCAGTGGAGAACCCCCTCCAGCCATTAGATGGTCCCGCCAAGGTCATCCATTTGTGAGCGATGACAGGATGACTGTTTTGTCTAATGGCTCACTGCATATCATTGCAGCACAGAAGGAAGATACATCTGAATATGAGTGTGTAGCGAGAAATCAAATGGGATCTGTGCTTGTTAGAGTTCCACTGACTGTCCAGG
Seq A exon
GTAGGTGCACAAAATACAGGGCAATAACTTTCAAAAGTAGATTGCAGCATTAATTGACAGTAACAACAAGACTTTATCTTATCCCTTCCGTGTATGAATTAGGTGCATGTTAATCCTGTTCTGAGATGTCTCAGTGGGTTTGTGCTTCATGCTGTTTTGTTCCTCTGATTGGACTCATCTAGCTGTAGATAAATAATAATGAAAGATCTTGAACTTGATCCCATCCCCAGAATATATATATATAACCATATCTCTGAAGAAAAGTATTTAGGAACATAAACTATTTCAGAGCATCTGAGGTGATCTCTGAACTGTAGTAAGGCATTTCTGCAGTAGTGAGGACATGAAGCAGGTTGGATTTCCAAGCATGGCTTCTGAAGTACATTTTCTTCTTTGCTCTCTCAGTCTAAGAGCTGTCCTCATAAGTACATATTCCTAACAGAGTACCATTTTTCCCACTG
Seq C2 exon
CAGTGCGTGGTGGATTTTCGGATTGGCTTGAATGGCAACCTTGCAGCGTAACATGTGGTCAGGGTGTTCAGAAGCGCGCTCGTTGGTGCAACAACCCCCTTCCAGCAAATGGTGGGAGGCCATGTGAGGGGCCTGACACAGATGTGCGCAGCTGCCACAACAAGCCATGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:86
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0767911=I-set=PD(97.7=96.6)
A:
NA
C2:
PF0009014=TSP_1=WD(100=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGGACCACTGTTGAAGCTG
R:
CATTTGCTGGAAGGGGGTTGT
Band lengths:
354-815
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]