GgaINT0000447 @ galGal3
Intron Retention
Gene
ENSGALG00000005141 | HMCN1
Description
NA
Coordinates
chr8_random:268761-270340:+
Coord C1 exon
chr8_random:268761-268859
Coord A exon
chr8_random:268860-270212
Coord C2 exon
chr8_random:270213-270340
Length
1353 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TTTTTTTTTTTTTTGTCAAGTTG
3' ss Score
5.88
Exon sequences
Seq C1 exon
ATCTGTGGGTTAATGATGAAGGAAGTTATGTCTGTGAAGCTGAAAACCAGTTTGGAAGGATTCAGTCACAGCCAGCCACAATCACAGTAACTGGACTGG
Seq A exon
GTAAGTCTGGTTAATGTCAGTGATACCAGGGAAAGGGAAGACTGGCAGCGTTTCCATACATGGGATATGCTGGAATAGGTAACAGTCTGGGGTTTTTTTTTTTTACAATGAATAGGATGTTAATGTGTTACGTACTTACACCTCTGTGTTTGTAGCAACGTTTACACAAATGTAGTCAGCCACACAAACTAAATCAGAAGATATTTGCATCAAATATTGTAATTAAATTCACTGAAACTTTCACATTATAACATTGTCTTTTTACCAGTTTAGAATAGTTCCATCTACGCTTTGTAACATGGACCTTAAAAATGATGCATTCTGTGTTCTGTTTCTTATTGCTTAGCAAATCGATTAAGGAATGAAAAATCACCATCATGATGAATGCTAATGATTTTCTACCATGTAATTTAAAAAAAAAAAAAAAGTAGCAGTGAACTTGCTTATTGCAATGCATTGCTACGACTGGGAAGGAATCTTAGTGATCCAAGAGGACACTAAACATCCTGCTTTGACAATGACTGTGTTTTCAAGGAGTTGTTTATTATCTTGGGCAATTGGCAATAAAAGGAAAAATAATGCTATGGAATGTATGAATTTGTGGGAAGGTAAGAATGGTTGTGTCCACCATCAAAGAAAACGTTGGTTAAATTAAAACGTGTGGTGAAATCTGTAATGCTGACGTTGTTTCGTAAAGAAGTTTTTACCTATTTAAAAGCCTCTTCAGTATTTTTCCCCAAGTAAGAAAACATAATATATCAACTTGGTATCCGTGGGAACATGAGCTTTCAGGGAAGTGCTGGACTGGATCCAGTTTCAGCTGGACAATGTCTTTTCTTTGTTGCTGTTCCTTAATCTTAGAATTACTGTACATGTATTATTCCAACTTACTTTTCTTTCCTATGCTACTCAATCCTCTGTGGGTTTTTTTTTTTCCTTTCTGTGTCACTGACATTTCAGATACCAGAGCCTTATCTGGTATGTTTTGTCCTTAGAGAACTATGTTGGCACTGTGGTGCTTTTTGTTGATTACTGTGTTTTTTTTTTTTTTTCTGAGGTTTTTTTTTTTTCCCCTCTGTAAATAGTATGGTTTTCACTGTAGGAAATGTTTCTAGATTGTGCTGGCTGCTCTCTATTTGCATAGTGCCTTGCATAAGCAGACTTTTGTCTGATACTGCTGCAAGAAATATTACTTGACAGGACTAGTAATAAAAAATCACATCCAGTACCTTACATATATATATATATATATATACACTTAAATATATATAAAATATGCATTTTAAAAATCCTAATTAATTCTCTCTCTCTCTCTCTCTCTCTCTTTGTTTTTTTTTTTTTTTTTTTGTCAAG
Seq C2 exon
TTGCACCTCTGATTGGAATAAGCCCAGCCACAGCCAATGTAATCGAGGGGCAGCAGCTCACTTTGCCATGTGTTCTACTTGCTGGAAACCCCATTCCAGACCGGAAGTGGATTAAGAACAGTATGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005141:ENSGALT00000008254:16
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(31.2=85.3)
A:
NA
C2:
PF0767911=I-set=PU(45.5=93.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGTGGGTTAATGATGAAGGAAGT
R:
CATACTGTTCTTAATCCACTTCCGGT
Band lengths:
223-1576
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]