GgaINT0000460 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:285268-287878:+
Coord C1 exon
chr8_random:285268-285422
Coord A exon
chr8_random:285423-287593
Coord C2 exon
chr8_random:287594-287878
Length
2171 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TGCTGTTGTTTTGTCTTTTGAAA
3' ss Score
0.49
Exon sequences
Seq C1 exon
GCCTCTGTTCTTGGGTGATCCCAATGTTGAGCTTCTGGAGAAAGGTCAAGTTCTGCATATAAAGTCTGCTCGAATGGTTGACAAAGGTCATTACCAGTGCAGTGCCACTAATGCTGCTGGCAAACAAATTAAGGAGGTCAAGCTGATCATCCATG
Seq A exon
GTGAGTTTATACAATCCTTGATCCAAGAAAATCCTTCAGTTTTGCACACAGGATTTTTAAATGGAGATGCTCAGACAAATATAAATTACTTAGGAATAAGTTAAATTTAATGCAAAAATACAAAGTAAAGTGCAAGAAGAATCAGATACAAATAGTCTCTGATAAAGAGCATTCCAGAAGATCTTCAGGTAGTGGTAAGTCATCTCTCTCAAGTTGGTGTAGTCTGTGGTCATTTATAATGAGAGAAGAAGCACTAGCATGGGATAACTATGTTAACATTCTTATTTTATGTAGCGTAGATTATACTTTTTGTGTTTTTACAAGCAGTTCAGTCTTAGCAAAATACCTGGGAAAAAGATCCATGCGATTAATTCCTGTGATTAGTACAGATAAGTTTAAGGAAAATGAGGAGATAAACAGTTGGGAAAAAAGGAAGGGAAAGATTCATGGAAACAGGAATGTGCTTTTGAAATAAGACTTTAAAAGAGACATGAGAAGGGGTTTTTTGTTTGAAAGACAAAGAACATGTGACAGCCCAGGCAGACCTGAAAACCATAGGTGTACGGTGCTAGCAGAAATGATGGAGGAAACATGCTGAAATCTATATATAGGATAAAACTGCTGGGCCCAGAGTGTGAATCATAGCTATTTGCATCCATGAGCACTAAAGCTAATGAGTCCTCATTTGCTATGGCTTTGAGTCTGAAGGTTTTGTGTCTTCTGTTCTGACAATGGTGAATTTGTGATACATTATTTCCCTCATTTGGGACATTTTTGAAGCATGGAGCAATGACATGCACAGAAATGTGCCTATATACTAATCACAGTGAAGTCTTCTGGGAACAAAGAAAATGCTGTGAGAACTCTCTGGTGATCAGGGTCATTGATGTCATAAGATTAGGGGAATAAAAACCACTCAGATCCCCCTAGGTGCATAGACTTCAGATTCTTCAGAGAAGAGAGGTGAATTAGTCTTGGCCAGACAAACAGAAGCCTACAGAGTAAGAGAGGAACCTAGATGCTGTTTCCCACTAGTTCTTACTTTGTTTTAGCTCTCTAGTTCTATTTTTATCTCTGTGGATGGAAGCATTTGTTGATAGAGAAATGCATTTGCCTTTGAACTGAATATGTTTCAGCATATGTTTTAGATGTGCATATGTTTACACACAGAATATTAATAAGGAAAGTATTTCATCATGGTTTGATAACCAGCAAGATCTGTCTCATAGGTGTAGGTCTGACACATAGGTTCACTGACACATTTCTTTACATTTCTGTGATGGCATTTTGAATGAACACTGTGGAAGTCAGCGGAAGTCTAGGATACGCTGAACATGTTTGGCAGGAGAGGAGTTAATGTGTCTGCCAGATGTGTCTGGTACTTTCAGCAGCTATAAATTTAGTTGTTGCCAATTTCACTGTGTTTTTATTGTTTCTACAAGAGATTTACGAACTCTTTATATTGGCTGATTTTACACAAGAGCTTGTTTGCTAGAAAAAATCTGAGTACTGCTGCCCAGTGAGTGAGGGAAATGACTGTGGGCCAAAAGCTTCAAAAATAGGAGCATAAAGCTGAACTATTAAGCTCATCTGTAGTCTCAAAGTAAGTGACTTAATCTTCAGAAATTCTGAGTACCGAGCATTTCCCACTCCAGTCATAGAGGTTCTTGGATGTCTTTGGTTTTAAAATTGCAGGTTGCTGTTCCTCACTGGGAGGATGCAGCTCCCAAGACATCCAGAATTTGCTTTCTTTACTCCTCAGAGAGAGGGAAAGGGTCAGCATTGTACCCTAATGCTTTGCAGGAGACATGGAGGCCCAGCAGACTTAACCTGGCATATGTTGGAGCCTCAAACACGAAGTGTTCTCAGGTACTTTTAGTGAGGCAGTAATGCTTTCTAGTGCCCCTTGGTGTGATGCCTGTTTATTAAATATAAGGTGTTCTTTGACAGTAGATTCCATTTGTGTTTGTGTTGTCCTCTCTTCATCCTTCCAGCTCGATGTGCCAAAGAGAAATCTACAGACACGGAAAAAAGCATCTCAAAAGCACCAGGAAAGATCAGAAGTCTGAATAACCTAAAATCTTTTATTCTTAGAACATTCTAATGTTAAAATTATTTAAAGCTGCACAGGCTTGTATACTAAGGCTTTTATGCTGTTGTTTTGTCTTTTG
Seq C2 exon
AAATAGTTCCTCCTAGTATTAAAGGAGGCAATATTACTACAGAGGTATCAGCACTTCTTAACAATCTTATAAATCTGGATTGTGAAACCAAGGGAATCCCTGTTCCTACCATTACCTGGTACAAAGAAGGACGCCGGATTATTTCCAGCCCCCAAGCTTTATATGTGGACAGAGGGCAGTTCCTGCAAATACCTCATGCCCAAGTGTCAGATTCTGCAAAGTACACCTGCCATGTGACCAATGCTGCTGGAGCTGCTGAGAAAACATATGAGGTGGATGTCTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:29
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:
PF0767911=I-set=PD(58.1=94.3)
A:
NA
C2:
PF0767911=I-set=WD(100=88.5)
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:
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]