GgaINT0000467 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:292065-293632:+
Coord C1 exon
chr8_random:292065-292166
Coord A exon
chr8_random:292167-293455
Coord C2 exon
chr8_random:293456-293632
Length
1289 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
TTTTCCATTTAATTTTACAGCTA
3' ss Score
9.82
Exon sequences
Seq C1 exon
AACCACCCAGCCTGGAGGATGCAGGGAAAATGTTAAATGAAACAGTGGTTGTGAATAATCCAATCCATCTTGAATGCAGAGCATTGGGGAACCCTCTACCAG
Seq A exon
GTATGCATCTTTCAGGATGTGAAGACTGTCTGATGACAGGTTGTGACTTTTCTACGTCTTTTGAAAATAATGATATTAGCATGAAGTTAATTTTGTGGTATTTAAACTAGCTAGAAACTATTAAACATTATTTATGACAGAGAATGTCAGTATATTGAGTTATGTGGAATAAGAATTGGGAAATTGAGTGATTTGTTCTGTTTTCTAATTAAATAAATGAAAAGCAAGTGGATAATCTACATCCTTATGCATACAGCAATGTTTTGTCCATAGGCAACGATACTGTTATAGTTTTATGAAATCATCTGTAAACCACCTTTAAACACATCTACTCCTTTTCCCCGTCAGGTCAATATTTTATGGGGTAGGGCAGACTTGAACAATACCTTCAGTATTGAGTGTACCTGTCAAATGGGGTCATATCTAGGACCTTGCCTAAAGTCTCTGGAAAACCATATGATTCTCTCTATTTGCTTCAGGCCTCTGGCATGTTTTCTGCAAATGTTTTGCATTCTGCAAATGCAAATGTTTTCTGTGTGTGTACCATAGTTTCTGTGGCTTTCCCGAATGATAGAGATTATACTAATGATTTTCTGGGTTCTCATGATATTCTAAGCTTTGTAAACCAGGCTGCTTGCATCTGTTTGTTCTCATCTAACTGAAGAGTGAAGCGATACCAGTAAAGTGTTAGTTTGCATAAAAGCTCTGCTGAAGAAGAGTAACATCTTTTGGCTGAGATGCAAAAATGTCCTCATTTTTTGTTGATTTTTCGTTTTATTAATTTTGTTCTGGAGTAATACCAGTTTTTCAGTTTTCATTTCCTATTTTTCAGCCTTTGAGATGAACTCTGTTATGGCTGCTTGCATTTTGAATCTAAACTTCTCAGTTGGTTCAGTTTAATGTAGCAATACTTCAGGGTAAATGGTGAAAAATGATACATACTGTGTATTTGTGTAGTTTTCAACCTTGGTATTAGATGACTAGACATCATCAAAATAGATGCTTTCTGTTACATTTTCTTAACTTCAGAACATTATTTCATAAGCACATGGTGTGCATGTACAATAGCTTCAAATTTGCTATTGAATCCTGTAGGCATAGTCATTATTTTGCACAGATGTTACTGATTTTCTCATTTCCTGGCTACTTTTTACTGTTATTAATTCTAATGAATATATATTGTGTGGTTGGTTTTATGTCTCTGACAATTCTGAGGGAAAATCTGAAGTATATTTGGACCTGTTTGTCAGGGGGAATACTTCTGACAACTTTTCCATTTAATTTTACAG
Seq C2 exon
CTATCACGTGGTACAAAGACAGTCATTCACTCACCAGTGCTGCAAGTGTCACTTTTCTGAACAAGGGTCAGGTTCTGGAGATTGAGGGTGCTCAGATTTCTGACACTGGCATTTATAAGTGTGTGGCTGTCAACATTGCAGGCACAGCTGAGTTGTCCTACAGTCTTCAGGTTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(31.0=74.3)
A:
NA
C2:
PF0767911=I-set=PD(67.9=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACCACCCAGCCTGGAGG
R:
CATGAACCTGAAGACTGTAGGACA
Band lengths:
279-1568
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]