GgaINT0000529 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:372169-373641:+
Coord C1 exon
chr8_random:372169-372231
Coord A exon
chr8_random:372232-373521
Coord C2 exon
chr8_random:373522-373641
Length
1290 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
AAAATGTTTCCTTCCTGCAGATG
3' ss Score
11.17
Exon sequences
Seq C1 exon
GAGATCGTAACAACCAGTGTCCTGCTGGGTTTGAGTTGAACTCATCTGGGCCTTACTGTACAG
Seq A exon
GTAATACGATGCAACAAGTTTAATATGTAGTCGGGCAGCAGCATCTTCATCCCTTCTGTTCAGAGCTCCTGAGCATGCAGGGCACACTCCAGGAAGTGGAAGCTGCCACCAATGGACAGATGTGGGCCCAGAACACAGAAGCAGGTCCCAGGCAGCCTTCCATCAGCATTGTGATGCGAAGTGGGACTGCTGAGCTGCTGTGCTCACTGAGCCTTCAGACCAGTGGAGCACTCTGAGAGGGGAGGGAGGAGGGCTGGGGGCCTAGAGAGCAGCCCACTGAAAACCAGCTGTTGCTTGGGTAGCAAATGTGAAAAGAAAGTTATGAGCATTTTAGCTGTCTCCTCTTGGTGACTGGATCGTGTTTGCTTCAGGGAGCAATACCTGATATGGTTTTGTAGACTTAATTCATTGCCCCTCAAAAGTTTAAAAATTAATGGAATTAATAAGGAAACTTTACACCATCAAGAAATTTTAAAATCAGGAAAGCTGAAAATACAGCTGCTAAACAGTTTTTCTACTTGCAGTATTTTCAGTAAAACAGTATGTGTTCAAAACTTACAATACAGAAAATGTAACAATCCTGGCAAGGCTGTCTGAGAAGTCTAAATAGAGCACTGAGTTCCATCTGTTCTGTTGCAGAGAGGTTCTCTGAAAGTGACTCTGTCAAACCTTCATTACCACAGCAGTGACCCATCCTGCTCATCAACTGCAAGGATCCCAGGGAGCCCATTGTGTGCACCTGATAGAACCAAGAAGCAAGATCTTAAATTAGACATGAAGGCTCTGCTGTGTGTGAATCTAGACCCTTAATGTACACTGAAATGTAATAAAGGAGGCTTCAAGGGCTTGGTTATTGTGATTACAAGTCATATCTCAATCATAGAACTTTCATGCTCTTATCCCCAGGTTCAGTCCTTGCTCACTTTCTCAAAGCGCCCAGGGATGACAGCATGGTTTCCTGGTGTGTGTGCCAGCAGCTACCTAGCATAGCTCTGCTGATCACTGGGACTCTGGCCAAACAAGCGAAGAATGTTTGTGAGAGCTGCCGGTGTGATGTGGACATGCTGCAAAGGGGCATTCCACATGTTGCTCTCACACCGCAGGAACAGAGTGGGGGTGGCAAGGTGCTGAGGACAGCTTGGTATGGAAGAGGATATGATGCTGTTTGTGAAGCTACCTACTTGCTAGCTCTAGCCTGAGGCAGACAGACATACAGCTCCTCTGAATGTCACTGGTGTTAAGTCTTGTAAGTCTTGTAAACAGTTTTTCAAAAATGTTTCCTTCCTGCAG
Seq C2 exon
ATGAAGATGAATGTGCTGTGCGAAATCCCTGTTCCCACACCTGCCACAATGCTGTAGGAACCTACCACTGCTCCTGTCCAAAGGGCCTCACCATTGCTGCAGATGGCAGAATGTGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:98
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:
PF126622=cEGF=PU(80.0=72.7),PF146701=FXa_inhibition=PU(4.9=9.1)
A:
NA
C2:
PF126622=cEGF=PD(15.0=7.3),PF146701=FXa_inhibition=PD(92.7=92.7),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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]