GgaINT0000535 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:379031-381872:+
Coord C1 exon
chr8_random:379031-379381
Coord A exon
chr8_random:379382-381752
Coord C2 exon
chr8_random:381753-381872
Length
2371 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAT
5' ss Score
6.62
3' ss Seq
TTCATGTTTCTTTCTCACAGACA
3' ss Score
10.47
Exon sequences
Seq C1 exon
ACATTAATGAATGTGAACAAGTGCCTAAGCCCTGTGCATTTCAGTGCACCAACACCCCTGGCAGCTTCAAGTGTATCTGTCCACCTGGACAACATTTATTAGGTGATGGGAAATCTTGTGCTGGATTGGAGAGATTGCTACATTCCGGTGCCTATTACAATATCTATAACTATGCTCAATTCTCCCCTATAAGAGACAACTATCAACCTCAACGGTCTTACAGGCACTCCTCAAACCTGTACAGCTCCTTCTCAGAGTATAGGAACAGCAGAATACCTGTCTCCAGAACTAAAAGGAGCATTAGAGAAACTTGTCCTGAAGGCTATGAGGCAAGAAATGACAGATGTGTAG
Seq A exon
GTAAATGTCAGTCATGTCTGTGCAGTTGTCTTGCTTTAGTCCTTCTTCTTAGGCTGCTGTTTCATATCTGTTAGAGGCCTATGGTCTGTGGTGCTCTGTTATTTCACATTACCATGTTAAGTACTCAGCAAGTTATGCATGTGTTTGTTTCTTGGGCAGGTTGTAGCAAAAATGTTTTCAAACCTCTTCCCTGAAACCTCACGTTTTAGTTGTGCTGCTTGCTATGTATTAGCAAATTGTTACCCTCTGTTCTCTTTATCCTGATGATGGTAGCTCACCTTTGCAAGTTTTCTCTCACTTAAGAAGCACCAGTAGGCCCCTCCACCTTGGGGATGTTGCTCATGTCAGGCTCCCACTTGTGGCAGTAGTAGTCTGGATCAAAAAGGCTTAGAATAAAGAGTGTAGAATTGAACATACTGAGACAGCACTGAGGTTGGTCACTGCCATGTGGGCTGTACAAGCAGAAGCAGTTAGGGGATAGAGCCAGTCATGCAATTCAGTGTGCAGTGGAGACGGATTATATGTAAGCAGACCAGAAGTTCATCTAGTCAGCAAGAGCAGTGCCGTTTCTTTCTGCATGATGAGGAGGGCAGGGCAGTTATGGTAACAGGCACATTCTGCCCAGGTTTTATTTATTTAAGAGATATGAAACTTCAGAACATACTTGTAAGACCAACAGGAAATAAAGGTGTATGGCACCTCTCTTGTTCCCTGAGCTCACTTTCTCCTTGCTCTGTGAGCATCTCTGAGGTTTTTCACCAGTACTGGAATGCTAATGCAACTCCTCTTGAAAGGTGAAAGGAATAATATCCTGCACTGTTCATTAACTGCTCTGCACAAAATGTTCAGACTAAATGTTCAAGAAAAGTCATTTTTTTCCACCTTAACTCATGTTATGAGTATCTTAAAAATAGATATATAAAATTACTCAACTATTTTTTGATAATACTGTTGAGTTCAAGACTAAGTGTAGCACAGTCTAGGTCTTTCAAGAACTTTTTCCAGCATGTTTAGCAACAGTTTGTGGTGTTATAGGTAAGTGCCTCAACCTGACATGTATGCCAACATAGCAGTGTGCAGTGTGCCTCCCAGATAAAACAGTAAGCTGAAACTGGGTTCTAGTCCCTGGAGCTATGACTGTAATTATGTAGCAGTATACAATGTTGAAAAATGTGAATGCATTTGTATAAATAATAATTACAGATAGGCAGAGATCAGAGTAATCTTGTATTTGCATTGTAATGACTTTTCAGTACGCTTATGAATACAGCATGTTATGGGTATAGCTGTTAACTGAAAGAACTCAGACTGCAGTTACTACTGCCAAAAACCTATGGCCCACAGCCCAGCTTCCAGTTCAAGTTAGTGAGCACTGCTGTAACTCTGCTTCACTGGAATAAATGTAGATTTAAGATTTACTGTTTAATGCAAAAAGACATTCACATAATTCTTTTATTTCCAAGAAGGTTCTTTGAGTAGAGAACTGTTAACGATTTGGTAACACACTTAAAATTTCTTTAGTCACATCTGTTTTTCTTTTCTTTTTGCATTTTTTTGAAGTGCAATCCCTGTAAATCAGACAGAGAAGGAATAAGCAAAGACCTTATTTACTCTGTTTCAGTTATGCAAGTCTTAATGCTTGCACATGGCAGTAACTTGCAGAGTTCTGCTGCTCTCCTGAAGTAGAAAACATATCAAAAGAAGCAATGATTAGATGTGATCTCTGTCTGAATCCCATTAGTCTGCTTTGAAAATATTAAATAGTGATCTGCTACTTACGTGTTTGAGAGGGAGATTTTAAAAAAAAAAGCTTAAAAGAGCATTTAAAGAGCATTTATGAATGGTCTTTGTGGTTAGTGAACTTAATTCGGCATGAGAGCAGTCAGTTTGGAAGGGAAGAAGTTTTGTCCAAGGAGGGATAAACTGTAAGAGCAATTCCCTGAGTGAGGGCCTCCTCTGAAGAGAGAACTGACCCCTGGGCACTTCCTAAGCATGTTGCCAAAAATATTATCAGGCAGCTTGGCATCCTGGGGCAAGACTGTACCCCTGTGTCCTGTGTGGGTTTGTGCAGCTCACTCATCCCCTTGTTGCCAGTGCTCTGTATCAGAGGGGTCTCTCAGCTCAGAGGGAGACCTAGTAAGGCTGCCAACAAAAGAGGCAAAGCTTTTAATTTTATAAAAGCTACAGGCAACAGAAGCAAGTAAGTTAGGAAAGGTTTGCTAGTTTTAGACATTCACGACCATTACCAAAAGCAAAAAAAAAAAAAAGAAAAAAAGATCCCCGTGAGCTCCACCACCTCTTCCCACATGCTTGCACACAAATAGGACATCAGCAATCCCGATGTTTATATTTTCATGTTTCTTTCTCACAG
Seq C2 exon
ACATTGATGAATGTGAAGCCAGAGATACATGCCAGCACGAGTGCAGGAACACCCTGGGAAGTTACCAGTGTGCTTGTCCCTCTGGTTATCATCTTATGCCCAACGGCAAAACCTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:104
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=33.9),PF126622=cEGF=PU(77.8=11.9)
A:
NA
C2:
PF126622=cEGF=PD(16.7=7.3),PF126622=cEGF=PU(83.3=48.8)
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]