GgaINT0000468 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:293456-297345:+
Coord C1 exon
chr8_random:293456-293632
Coord A exon
chr8_random:293633-297193
Coord C2 exon
chr8_random:297194-297345
Length
3561 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
GCTTTATTTTCTTTTTTCAGTCC
3' ss Score
9.55
Exon sequences
Seq C1 exon
CTATCACGTGGTACAAAGACAGTCATTCACTCACCAGTGCTGCAAGTGTCACTTTTCTGAACAAGGGTCAGGTTCTGGAGATTGAGGGTGCTCAGATTTCTGACACTGGCATTTATAAGTGTGTGGCTGTCAACATTGCAGGCACAGCTGAGTTGTCCTACAGTCTTCAGGTTCATG
Seq A exon
GTAAGTATTACAAAACTTATGAGAAACTCCTACCTGCACCATGTTTGCTCTTTTAAATCTTCTCAGAAGTCTCGTCACATCATCATCCTGGAAGAGATATAGCAGGGCTCAAGGGAGCACATTCACTCCTTGTTGTTGTTTTTTCCCTTAGTGATATTAGGATACATGTTTTTAATATTAGGAAGATGTCATAAGGGAATTTGATTTTTAGGAAGAATGAGCAGAGACACCAGAATTGTGGAAAAGATATTTATATTATCATTTAAAGAGTTCAGAAGGACTTGAAATTGCTGTGTTTCACTGTAGATGACTTCAAAGTCTACAGTAGATAACGAAAGGACACAAGTCAAGTGTTTTTTCATAGTGCAAGAATCTTAAAGAAAAATGTACTGTGTTTAAAGAGGCGAAGTCAAAGTGTAGGTGTTTGCAGAAATGCGACACCTGATCAAAAGCCAAATAGCAGCTCTTCCACTGATTTCAGTGGATTTTGGATCAGGCTCTAATCCAAACTCCTATTTCTGATGCATGCGTATGCATGTAAGTGGTTTTCAGTGGGCATCTTAAACGCAAAACTGTGGCCCAAATTTGGCACGGTGTCCCAGGCTGGTATGCATGCTTAGTATGTAGTTCCTATTAATGTTAATTAACAAATATGGAGTTGGGCCATACATTTCTGTTAGATTAATGACTGTCATGGGAGAGAATGAGGGCTCAAGGCATGGTCAAGGGCAGTTAACCTCACCCAGTGATGAATTCATAGGAAATATTTAGAGCCAAGGTCATTATACTGTTTAAACTGAGAAATAACTCCTAAGTATATGTTTATCTTCTTATAGGTAGTGGAATTTCAGCAGAAATTTACAGAGTTTTCTAAGGAATTAATACTCTCTCACTTAGTGGCTAACACTACACAAATAAAAGTACTTCCCCTACTGGAATAGAAATATATACAGTTGCAGCCAGTGCTGATTGCATCAAGGGAAGCTGAAACACCTATCTATGAACCTTCTTAATTCAGCTTGTGTGGTGCAAAACTTAAAGGGAGTGCTTTTTGGATTTACCAAAAATGAGGTTATCATCCAGTTTATTTGGAGTTTGAGTTTGGTAAGACAGAGGGGTTTTTTTGTTGTTGTTGTTTTTTTTTTTTTTTTTTTTGTTGTTAATAATGAAAGCAAGAATGACTACTAAAGGAAGAACAGACTCTGAAGTGTCATACAGAAAGTTGCATCAAATTTACTGATAGCCTGCTCTGTGTTTTTGTATGGCAGCTGGCCCTGTGAATGAGCATCTATCTTGGTTGACTGCTGGTTGTATTCAACAGCTTCTGTTGTTAATAGAGTGTTGTGGATGCAGTAGCTGTGGTAGAAATTATCAGCTCATTTTTGCATTAAGAAAAAGGCCTGATACCACACACTTAACAACTAGGCAGGCCTACTCAGTTTGAAGGGAGCAGGTTGAATTTTGGCTTAGTATATTCTTATGATTTCATGGTACTAAGATTTTTGCACTTCTTTCTCACCACTTCAACCTTTTCCAACATTTAAGAACAGCGGATGCTGCTGAAATAAGATGGAGATACTGTGTGTACATTGAAAAAAAGAGTATAAAATCATACTTGCATGTTTCCTGGGTTATCTGCTATTAATGAAATTCGTCTTAGGATGAGTAGCCTGAGCTGCATGCTGTTAGAGACTGCTGAATTTATTAATGCATCTCATTTTCATTAAAGAATACATAAACATTTTTTTCTCATGTCGGATATATATGAGTAGAATGCACTGTTCTCATCTTTTTCTAGGAGTGACTTCAAGCATTAAGCTTTTGTGATTGATTTGAAAAGTGTGAAAAGTGAAAGTACAGGTATATGACTAAGTTTTAAGTGGTGGAAGCAACATTGATTTATCAGGAAAATCAGAACAATGTTCTGATTTTCCTGATAAATGAAACATCTCTCTTTTTTAACACTTAAGTTGCAAATGTTGAATGTCTGCAGAAAACAGCTTTTTGATTCCAAAGCTGTTGTTTTCTCCTGTAAATGTATGCCAGTGTTATGCCCACACTTGTTTGCTCATGAAGAAGTACAGAAATAACAAAAGAAGTATACTGGAAATCTCAGGTATGTTCCTGTCTCCCTTTTAAACATAGTTCTACAAAATTTACGAGGCCTTACACTTAAAATAATTGTTTTGATGTGTCCCATTAAGATTATTTTTATCATCAGACAGGCAGATATTGTACGGATGGAACTGGTAAGTGTATTTTCTGCAAGACTGATTTATTACTCTGTATATATTTGGTTTATTCGGTTTATCATATAAACTTCTCTAATTAATCTCCACCACTGTTAATGCCTTTCATGAGGTCTAGATGGAATGTTATAAAAGTGAGGGAATATTTTCAGGTTTGATGTTCTGGTTCCTGGGTGTCATAGCTGTTCTCTGGGCTGCAGACTTGATCCTACTTACCTTGCTGACAGTAGTTTCACCAAAGTTATCTGACTGCTTATGTAAGTAAGAGCAGCATTTGGCACAGAGCAAACAAATGGCAGTAGTGCTAATGTTAGAAATCTTTCCAACAGTATAGTACCTTGCAGGAAGAGAAGCAAGTTCTAAAAGTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCCTTTCCATGAAGTCCTAGAATGGAAATGTTATAAAAAGTGAAGGGAATATTTTCAGGGTTTTGATGTTCCTGGTTCCCTGGGTGTCATAGGCTGTTCTCTGGGCTGCAGACCTTGGATCCCTACCTTTACCCTTGGCTGACCAGTAGTTTCACCCAAAGGTTATCTGACTGCCTTAATGTAAAGTAGAAGCAGCATTTGGCACAGAGCAAACAAATGGCAGTAGTGCTAATGTTAGAAATCTTTCTAACCAGTATAGTACCTTGCAGGAAGAGAAGCAAGTTCTAAAAGTAAGCATCCCATTTAATTTCATTTTGATTTATCTTAACTCTTACATAGCTGCTCCGGCTTTATTTTCTTTTTTCAG
Seq C2 exon
TCCCACCATCAATCTCTGACAGCAGTGACACGGTGACAGCGGTGGTCAATAACCTTGTGCGAATGGAGTGCGAAGCAAGAGGCATCCCTGCACCCATCCTGACATGGCTAAAAGACGGCAGTCCTGTTTCCAGCTTCAGTGATGGACTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:37
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(67.9=95.0)
A:
NA
C2:
PF0767911=I-set=PU(53.9=94.1)
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]