GgaINT0000533 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:374799-375615:+
Coord C1 exon
chr8_random:374799-374927
Coord A exon
chr8_random:374928-375486
Coord C2 exon
chr8_random:375487-375615
Length
559 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TTTTGCCCTGTTGCTTACAGACA
3' ss Score
9.1
Exon sequences
Seq C1 exon
AAGATGTAAATGAATGCAGGCAGAATGTATGCAGGCCTGATCAGCTTTGCAAAAACACCCGTGGTGGCTATAAGTGCATTGAGCTGTGTCCAAATGGAATGACCAAAGCAGAAAATGGAACTTGTATTG
Seq A exon
GTGAGTGGAAACCTAGTGTACTGTATGGTGATGGTAAGCACAGGGACAGCAACGAATGGTTTCTGAAAGAAAAGTCTTTGTAGTGCATTGCTAATTACTAGAATTTGTACATATTAAGGCACTGACCTTTTGATTTGTGGGAACACAGGCATTTAAATTTTCTTTAAATTAACTGGAGAAATAGACATATCTTTATCACCTCCAAATTTTCTAGATTATATTTTATTGGACTGAACAGCTACTAGAATTGGAAACCTAAATTAGAAGTTTTGAAAATTAATGGAAAAAGTAAACACAGTACAATTGAAAAATCTGCACGTATGCTCAGAATCTGCTTTCAGATTGTGAAATGCAGATAGTTTCACAGATCTGTAGTGTGCTGTTACAGAGTAATTGCTGATCATGGTAGCAAGTGAGAAAAGACTGTTCAGAGGCCAAATCTATCGAGAGAGCCAAACTCACTGTGGTTTAACTGCATTCATTACACATTAAGGAATTTAAAGCTGTAGGAACTTTCAAGAAAATATCTGACTACTTCTTTTTGCCCTGTTGCTTACAG
Seq C2 exon
ACATCAATGAGTGCCATGACAGAACCCATCAATGTCACTACAACCAGATCTGTGAGAACATGCAAGGGAGTTACCGCTGTGTGTGTCCAAGAGGGTATCGGTCACAAGGACTTGGAAGGCCTTGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:102
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:
PF0764510=EGF_CA=WD(100=93.2),PF0764510=EGF_CA=PU(0.1=0.0)
A:
NA
C2:
PF0764510=EGF_CA=WD(100=95.5),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTAAATGAATGCAGGCAGAATGT
R:
CCACACAAGGCCTTCCAAGTC
Band lengths:
254-813
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]