GgaINT0000518 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:359714-360114:+
Coord C1 exon
chr8_random:359714-359887
Coord A exon
chr8_random:359888-360094
Coord C2 exon
chr8_random:360095-360114
Length
207 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
TGAAAATATCTGTTTCTTAGTTG
3' ss Score
5.03
Exon sequences
Seq C1 exon
CAGTGCGTGGTGGATTTTCGGATTGGCTTGAATGGCAACCTTGCAGCGTAACATGTGGTCAGGGTGTTCAGAAGCGCGCTCGTTGGTGCAACAACCCCCTTCCAGCAAATGGTGGGAGGCCATGTGAGGGGCCTGACACAGATGTGCGCAGCTGCCACAACAAGCCATGTCCAG
Seq A exon
GTATTTAATAGATTGATATTTTTAATTTGCCTTACGTCAGGTGCCTCAGTAATATACAATTTTCACCAGGGATCTTCATGACAGATGGATTTTTCTGACAGGGTGAAATTCATCTTGAGTTTTGTGGAAATTTATGCACACACAGTTTTCTGTTTCTTTGTTTGTTTTAAATTATTTTAATTAAAGCTGAAAATATCTGTTTCTTAG
Seq C2 exon
TTGATGGCAACTGGTCTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:87
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009014=TSP_1=WD(100=86.4)
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:
TGCGTGGTGGATTTTCGGATT
R:
TTCAGACCAGTTGCCATCAA
Band lengths:
191-398
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]