GgaINT0000476 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:311134-314305:+
Coord C1 exon
chr8_random:311134-311301
Coord A exon
chr8_random:311302-314191
Coord C2 exon
chr8_random:314192-314305
Length
2890 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TTGTGTATTTTTGGCTTCAGGGG
3' ss Score
8.06
Exon sequences
Seq C1 exon
TTCCCCCAGATATTGCTGGTGACCTTCAGTTGCCTGAGAACATCAGCACTGTGGAGAAGAATCCCATCTCTCTGGTTTGTGAGGCTTCAGGAATCCCCTTGCCATCAGTAATGTGGCTCAAGAATGGATGGCCTGTCACTTCCAACACCTCAGTGCAAATCCTCTCAG
Seq A exon
GTACAGCGCATTTAAAGCTGTAGCTATTTTTTTTAATAAGGGAGTGTAGTGAAGGCCCTTCCATGGTGTGAACATTCCACACACAAGAAAGTTTGACTTAGTAATCCAAATTGGTTGCAGCACCTGGTAAATAGCTAAAGTACACTAGGAAAGATGTTACCAAATCTTACACAAGTGAGCTGAAAATGTGGTAACTGGTCTGCATCGTGGAATTAAGCCATATTTCTGGCTGTTACTGTATGTCAGTCCAGTGTGTATTTCCAGAAATGTGTCAGATAACGACATCTTGCGGAGAAACTTAGCATTCGCAGTGGGGAAAACAGATATGATTCATAGGGATCTAGTTTTTTAAGCCAGCTTCACCTACAAAGAACTAGTACCGATGCCTTTTATGACAAGTAGCAGTTGGCAAGAAGTATCTGAAACAGGAAGGCCTTTGTACCTGTTCCTGTAAACCATCATTTTTGGCAGAACTGTAGGGAAGTAAGAGTACTGGACTGGCAGCTGCAGTTTTGTTAGAGCTTTATGTTTACAGTAGGAAATGGAGTTAGCAGTACGTGAGATTACAAATGGAAGATGTGTACCAAGCAAGCAATAAATTTTACATTAACATTTTGTGTCCTGGGCTCAGCTTTATGGACTGTATAGAAGTAATTAAGTATTTGTGTACAACTGAGATGTATGGACAACAACTGGAATGATTCTTTGGTTTTGGATGTGCCACTCACAGCTAGAAATCGCTGTTTCTAATACTCCACTGTAGCTACCAAACCATCCTATAGCATGAGCATGAGAAAACTATCAGAGAGGTAAAGAAAGTAAAAGGTACGTACAAGCTCAACTAAGACTGAATTTAAAGCTGGAATTTGTCAGCATTTTTTTCCATCACTGTAGCTTTTGACATTGCAGGTAGTCCCATTTTCTGCTTTTTTAATTCTAACACATGGAGAAAGGGGTGGGTGATAATTGTGCTGTACAGACCTGGCCATTTGAGTTGGTATTCATTCCTTTTGGCACACAGTTGCCATCAACAAAAATAATGTCTTCTGGACTTGAGTGTCCCTATTCTGCCTGTTGTTTTCTACGCCCCCACTAGTATCACCACCCAGACTTCAGAGTCAGGACGAATGAGATAAAAAAAATGTTATCGTCTCTGAATGTTAGCTGTAGTGTGAAACTGACCAGAACTTGGTGCTTTGTTTTCCAGCAAACTTTGTGCTTTTGTATAATTCTTCAGAAAACTACATCTTGTGGTAGTGAGCTGGGACCAACATGGCATTTGAGACTGTGTTTGTGTTTGTACAGTGGTAAAAAAAAAAAAAAACACAAAAAAAACCTCTTCGACTAATGCTGAGAGGTAAAATACTCTGGCAAAGTAAGATTTCAGTTCTGTTGATTGAAAAAATACATGGCATTGTAGATGATTTGAATGTGTGGACACACTGCTGTCAACTGTTAGTCTGTTAATTGAGATACTATGCAGGTGTTTGCTTTTGAAGATGCTTCATGTAGTTCCTTTAGGAAAAAAAAAGAAAAAGTTTAACTATGCCACCACATCTGCAATTCTTGCAGAGGTAGCTTTAGGAAGGAGAGACACTTTTATTAAATTGTAGTCAAATGTGGAGAATCGTATCCTGCCTCAGCACTGGAGCTCTGCGTGTGCAAGTGTCTGAAAAAGCAGACAGGTATCTTCTTTGTGTTGCATCTTACGTGGCTTTGTTTAGGGTGTGCATGGGAAAAGGGATCAGTGTGAAATAAGAGTGCAAGAGAAATCCTTCCTCAGTTGCACAATACTCCCTCCAGCAAGTGTGATTTCTTGAGTGGACACACATCCACCAACCAGGTTAAGCAGTTTCTTCCTTCAAAGCACAAGGTCAGGAATGTAAATTTCTGGAATACATCCTGACTATGAGATCCTGTAGACGTCTGCAGACGGGAGCTGCACAGTTCAGATGTGATGTCCTGTGTGGTAATGATTGCTGATTTGAGAGCAGTTGATGAGAGACTGGAAAAGGCTGAAGGTTGGCCACTACATTTGTTTTTACACTTAAATGCTCGTTGATGCTTGTTTTGCTGTTCCTCTGCCAAAAAAAGAAGCAAAGAGAAGTTACTCTTCTAGGTCAATGTTCTTGGTCCTCTGATCAAACATACTTAAAAATTATATGTATGTGTTTATAAAATAGCTTTATTTTTGTGTGTACCCTCTCTCTGCTTAATTATTTTTCCTCTGTAGTCACCTGGATTCTCGGTACAGTAAAATACGTAAGTGAAAGTCCTGCTTTCGACAGTGGATTTTGTGACAGTTTTCTGTACAGAAGTATGAGCACAAATCCCCCATTCTGCAAACACAGTCTGCCTGCTGTATCCAAAGTTTATGCACGAATCTGAAGAGTTTAATGCACACCCCTGACATATTTATGTGCAGTCTGAGGGACCTGTCTATAGCAGGTTGGATTTTCTCTGCATGATCTCTGTAAATGTGTCTCAGAGTTTTCAGTGATACCAAGTTGGTCTGTTGACTTCCTGCATAAATTCTTGACAGACGTCTGAATGCATCAAAGTTCACTTGAACATTAAAAAAAAGGAAAAAAAAGAAGGGATATATCAAAGTAATTTGGAAGTTACTGAATAGAAAAAATAGTGTTATGAATGTTGAATGCAAATCTACAAATACTGAGGATTGAAGCAGATACACAGAAATGAAAGGAGCAGGAGGAAGGTCAGTCAGTTTCTCTTACTGTTTGTTCAACAAAACTAAGCACATTAAAAAAGAGGAGAATACGCTTGTACGTTTTACCAAAACATAAAAATTGGAAGTAGCGTAGACAGCTGGGGAATGTATTGGGTAGTGCATTGCAGGGCTTTAATAATTGTGTATTTTTGGCTTCAG
Seq C2 exon
GGGGTAGAACGCTTCGTTTGACACATACGACTGTATCAGATGAAGGGCACTATACATGTGTGGTGACCAACGCTGCAGGAGAAGCGAGGAAGGATTTTTATCTTTCTGTTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:45
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0767911=I-set=PU(56.5=84.2)
A:
NA
C2:
PF0767911=I-set=PD(42.4=92.3)
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]