GgaINT0000475 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:309367-311301:+
Coord C1 exon
chr8_random:309367-309648
Coord A exon
chr8_random:309649-311133
Coord C2 exon
chr8_random:311134-311301
Length
1485 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCTTTCCTCTTTTTCCACAGTTC
3' ss Score
11.61
Exon sequences
Seq C1 exon
CTCGCCCAGTGATACTGGACAGTGGTAGCTACCCATCAGAAGTAGTTGCCGCCCAGGGAAGTGAAATTTCCCTAGAATGCAAAGCTCAGGGTATTCCAGAGCCAGCAGTAACATGGATGAAGGATGGCCGTCCACTGGTCAGTGGAAGGGACGTAGCAGTACTTCATGATGGGCACTTTCTTCTACTGAGAAATATCCAGGTGTCAGACACGGGTCACTATGTCTGTGTTGCTGCCAATGTGGCAGGGCTGTATGACAGAAAATATGATTTAAATGTTCATG
Seq A exon
GTGAGTATGCAAAACGTGGGGCACGTGTAACAGAAACAAAGCAGGCCTTTAAGTTCACCTGAGGATATCCAATAAATACTTGTGTATTCAAACATGGTGACTCTATTTATTGTAAGCTTTATACATAGCACACTTCAATCTGCAGGTGTATCACAAAAATTCATATCCAATTTTGTTGTTCCTGAACATTATAAAATCTTATTTCTGTCTCTGTTAATACCAATACCAATGCATCCCCCCAGCAGCTTCATCTCCCAAGAATAGAAAATCAGGATACAGTATAGTTTTGTGTGATGTTAGGTCCAATTTTGTGATAAGGAAGTGTTCTTTCGGATTCTGTTATAGGAGGAGAAGTTAGGGTTTAACCAAGAATGCCACATTTGTGGCCCCCACCAGAGGACAGTTATGTGAGCATAGCCCATATCTCAAGTTTCTAATCATCAGATTTTCTTGTTTTGTGCTATTGGAAGGATTTAAGATGGTACCTCCAACTATAATTCATTTTGGTAATTTGACTTAATTGGATTGATTAGAAAATCATGCCCCATTAGAGCCATTCTAACTGAGAATGGCGCTTCTTTTGCATATGATTTTTAGTGCTTCATTGAACACTGAATATTTGTGTTTAGAAAGGGTAGATCCAAGAAAGAAAGAGGCATTCAGGAGTTACTGTGCGAATGAACCAGGACAGCAATTTACAGGAATTTAGCTGCAGGTTCCTCTGCAAATCCCATCGTCTCACAGAGACTTCCAGTTTTATCTGTAAAGTAATTTTATGTCTGATATCTTGCACTGAAGTGGGAAAGCTTGTACAACAATCGGGAATGGTTTGGGAGAGTATAAAACACAGTATAGGATGAAAATAAACATATGAATTTATCATTATTGAAAACAAGAGGCCAAAGTGAATTACCCAAATAATTTTGTTTTACTTTATTTGCTGTACTGTATTATCAAAGTTCTGGACAGTAAAAAGAAACTTTAGATCTTCTCAGGCTGCTTAGTCTAGATGATGTTCAATTCTTAAGCCCAGGTTTTTTTGTTTTAACGAATGATCTACGGAACTGAAATTACTTTTACTCCTAGCAGAGAAAATCTAAAAACAAATTTGAGGTAGTTATTTTAGTAGAGGAATTGTTCTTTCCATTAGCAAAATAATTCTGTCAGTCTTAACATTAGTGTTTCATTAGTGTTAACATAGTGCTTCATTCAGTACTGGAAATCGTACTTAATGTATAATGGATAGGACTACTATAAATTGTTATTTGCTAGGGATCTTAAGGCATTAAATGAAGGTAGTGATACTCATGGAATTAAATTTTATTTTTTCCACATAGTTGCACAGAAAAAAATACTCATAAGTTTAACAGTTTTGTAGCTCCTCACTTGCCAAGCTTATCTTTATTTGGTTGTCAGAATATTTTGAGAGAAAAATTAACTTTCATTTGTTTTGGAGTGTGACTTTTCTTTCCTCTTTTTCCACAG
Seq C2 exon
TTCCCCCAGATATTGCTGGTGACCTTCAGTTGCCTGAGAACATCAGCACTGTGGAGAAGAATCCCATCTCTCTGGTTTGTGAGGCTTCAGGAATCCCCTTGCCATCAGTAATGTGGCTCAAGAATGGATGGCCTGTCACTTCCAACACCTCAGTGCAAATCCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:44
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=0.018
Domain overlap (PFAM):
C1:
PF0767911=I-set=WD(100=89.5)
A:
NA
C2:
PF0767911=I-set=PU(56.5=84.2)
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:
CCAGAGCCAGCAGTAACATGG
R:
TGCACTGAGGTGTTGGAAGTG
Band lengths:
344-1829
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]