GgaINT1017234 @ galGal4
Intron Retention
Gene
ENSGALG00000002273 | LYRM1
Description
LYR motif containing 1 [Source:RefSeq peptide;Acc:NP_001155848]
Coordinates
chr14:14972896-14975089:+
Coord C1 exon
chr14:14972896-14973054
Coord A exon
chr14:14973055-14974996
Coord C2 exon
chr14:14974997-14975089
Length
1942 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
TTAACTCTCCGTTATCTTAGGTG
3' ss Score
7.84
Exon sequences
Seq C1 exon
ATGACAGCAGTCATGCGACAAGAAGTGCTGGGCCTCTACCGCAAGATATTCCGGATAGCCAAAAAATGGCAGTCAGCATCAGGACAGGCGGAAGAAACTACTGCAGAGAGGGAGTACATCATAAAGGAAGCCAAAACATTGTTCCGAAAAAATAAAGAT
Seq A exon
GTAAGTGTGTGTCATTGCAGGTTTCAGTTTCTGACTCCTTTTGTTGTGCTATGCACGCTCCTGGTGGCTGGATGCCAAGGTATGAATATAAAAAATGATTTCCCAGATTTCCTTTGCCATAAATGCTGGTACAAGCACATTTTAAGGCATATTTGAGTTACAGTTTATTATTTCAGGGGTGATATTTGGTAAGAAAACTCAAACCCTCTGAGATTTCCATTAACTCCTGCACAAGGTCAGGCATGTCACCTCGATGAGCACTGCCCGTACTGCGCACTGTGCTGCTTGGTGAGTGGATCCAACCACTGCCATGACGACTCAGCCAACCTCCTGCCATCTCCCCGGGAAACAGAGCCCCAAAAATGAAAAGTTGTGGTTGAAGGATGAGAGTTCAATAAAAAAATGGACAGAGGAGTACTTTTTTGCCAAGACAACTAATATGGCACTGCTTAATTTGCAAGGAAATTGTGTCTGATTTCAAGGATTACCATTTGAAAAGTCGTTATATGCAAACACATGCTGCAAATTCAGTGCACACCAAGGAATGTATTGTAAAGACAAACAGCAGAACTGAAAAAAATGTCTTCTCAACATTTTTTTTTTTAAAGTTACACCTTAGATGGACTCTAATATAAAAGCTTGTTATGTGGTAGCAAACCTGATTGCAAAAACATCATACACACTGACTGATGGTGAGTTTATTGAGCAATGGACAGAAAGTGTGGCAAATACAATTTGTTCTGATTAAAACCCACAGTTTTCTAACATTGGTTTGTCTCACCAGACTGTAGTCAGGTGAAGTGCAGAAATAGGAACATCTATCAGATGAAATTTGGAGGGTAGAGCTGCTAATTTCAAATTTTAACTTTTGGTGATAGATGAAGGTACTGATGCTACAGCTATGCTCAACTTGTTTTCATTTGAGGTACTGAGAACAAATATAATGTCCTTGAAGAAATGGCTGCTTTGGTGCCATTAAATGGCACAACTCAATTTCTTGATTTGTATGAAGCTGTACAAACTACATTGAAGTTATTTTCTTTAACCTTTGTCAACATATCTGGTACAGCTACTGATGAAACCTGGCAATGGTTGGTAAAAAAAAAAGAAAAGAGGGACTTAGAAAATTGATAGCAGGACTGCTCTGAAAGCAGTGCCTTCTATTGGAGGCAGCTCTGACTGTTGGTGGGATGGCAGCAGAGGTTGGACTCCATTACTTTTTATTGCCATGTGACAGATCTGACAGAATGGTGTCTGACATGGAAGTGTAGATGAAGGAAAGTGGTGTCATTGAATTCCTCCACCTGGAAAAATGGCACCCACTGACATTCATCAACACTTGTGAACACTGATGGAGATTTTTCTTTACCAAGTAGTGTTACTTTGTTCTTTGTAGCTGTTGTCGTTTCCTTGGAAATAATTAGGAGGCGTTCTATCAGAGTGCCCTCTGCAGCCATCTGTCACATGGCAACAAAATGAAATAGGAGGCATTACTTTTGGAGCAGGCATTGTAGCCCAATTCAGTGCAGGACTAAATTCAGCTGATACAAAAATCAGAATTAAGTGCAAATGAACACTACGTTTCTGACTTCAGTGTGAGTTTCAGGACAGAATGACACTCACGTGTCGCCCCTTGTTGTCTTGCAGCGGATGAATGCGTGAGCGTGCCTTTTCATGGAGGTAGTGGTAGTTTTTGCGTGTATTGTCTTTTTTACAGAGAAAACACCAAAGTTGAGTAAAACCTCTTCTACTCTCACAGTTCTGATAGCCTCTGGGCACTGCTACTCAGTGCCATTGAGCTCAGAAGTGCAGATGTGAAAAACACCATCACTGTATCCTTGGAACTGCAAAAAGGAAGGGAAGGGAAAAAAAAGGTTTGAGTTTGAAATGCTGATTTTTGTACTTGTACAAAATATTTATTTTTAACTCTCCGTTATCTTAG
Seq C2 exon
GTGATGGATCCAAAGCTGATTAAGCAGTGCATAGACGAATGTGAGGCAAGAATACAAATTGGACTTCACTACAACATCCCCTACCCAAGACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002273:ENSGALT00000003565:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0534710=Complex1_LYR=PU(68.7=86.8)
A:
NA
C2:
PF0534710=Complex1_LYR=PD(28.4=61.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTCATGCGACAAGAAGTG
R:
AGGTCTTGGGTAGGGGATGTT
Band lengths:
246-2188
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]