GgaINT0000500 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:344550-345512:+
Coord C1 exon
chr8_random:344550-344631
Coord A exon
chr8_random:344632-345375
Coord C2 exon
chr8_random:345376-345512
Length
744 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TTTCTTAATTTTTGTAACAGTTC
3' ss Score
7.53
Exon sequences
Seq C1 exon
GTCAAGGATGCAGGAAGATACACATGTTTGGCATTTAGCCCGGCAGGGGATGATGATAAGGAATATTTAGTAAGAGTGCATG
Seq A exon
GTAAGTTTGAGGAATATTTCTTTCCTAAATTAAGCTGTAAACTACAAAGGTGTGTATCACATTTAACAGCTTACTTATTATTAAAGAAGTATGTGTTTTGAGAAAATGATATTATACTATGTGATAATTAACATTTCTGACTATGGTTAACTCCTTTGACATGAAATAAAAAAGGAAAGTTTCACCTGATGCAGTTCATGCCTTCTGTTGTGAATAGGTTATAGATATCTGTGTTCTGCATCTTTGTTCAGCTGTACTGAATTTATTATACTTACAGAAAACTATAAAGTATACTGATACCTAAGATCGTAGTTTTTAGTAGAAAAGTATATATATATATTTAGAATACATTAAATGTAATGTCAGTAAAGGCAGTATAAACAGAACTTCTGCAGTTCTGAAGTATGCTTCAGGTTTCTTCTTGAGGGTTGTAACTGCCATGTTTCATGATGAAGAATTTAAGGAACTTCTGTGGTCTCTGCTCTGTCTGGCTTTGATTCTAGTGCCCTTGCTGAGAATTGATTTTAATTTAATTACTGTTGCAGTAGTTTCCAGTATGCGACTTAAAAAACAGTTTCACCAGTTAAACAAATGTGGTGTATTTAACACAGATATTGTAAAGTAGTACTAAATTGTGTAACTGTACCTTTGTCTTAAATATTGAGAAGTAAAATGCTTTTTTTAAAGTATGGTTTTAATGGTAGTTCATAATGTGGTGTTTATTTTTCTTAATTTTTGTAACAG
Seq C2 exon
TTCCTCCTAATATTGCTGGTACCAGTGGTGTGCAGGACCTCACTGTGTTGCAGAACAGACAGATTATACTGGAATGCAAGTCAGATGCTGTACCACCTCCAATAATCTCATGGCTTAAAAATGGAGAACTTTTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:69
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(29.4=89.3)
A:
NA
C2:
PF0767911=I-set=PU(46.6=89.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAAGGATGCAGGAAGATACACA
R:
AAAGTTCTCCATTTTTAAGCCATGA
Band lengths:
214-958
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]