Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L18a.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g1710 g1710.t11 TTS g1710.t11 12637218 12637218
chr_3 g1710 g1710.t11 isoform g1710.t11 12637362 12638250
chr_3 g1710 g1710.t11 exon g1710.t11.exon1 12637362 12637520
chr_3 g1710 g1710.t11 cds g1710.t11.CDS1 12637507 12637520
chr_3 g1710 g1710.t11 exon g1710.t11.exon2 12637608 12637941
chr_3 g1710 g1710.t11 cds g1710.t11.CDS2 12637608 12637941
chr_3 g1710 g1710.t11 exon g1710.t11.exon3 12638233 12638250
chr_3 g1710 g1710.t11 cds g1710.t11.CDS3 12638233 12638250
chr_3 g1710 g1710.t11 TSS g1710.t11 12638284 12638284

Sequences

>g1710.t11 Gene=g1710 Length=511
ATGAAAGCAAAAGGAGTGCTCAAAGAATATGAGATCATTGGCCGCAAATTGCCAAGTGAA
AAGGATCCAAATCCACCTCTATTCAAAATGATAATCTTTGCACCGGATCACATCGTAGCC
AAGTCTCGTTTCTGGTATTTCTTGCGTCAATTGCGCAAATTCAAGAAGGCCACCGGTGAG
ATCGTGAGTGTTAAGCGCAAATATGAGAAAACTCCACTCAAGATCAAGAATTTCGGTATC
TGGCTTCGTTATGACTCGCGTTCAGGAACACATAACATGTATCGCGAATACCGTGATTTG
ACAATTGGTGGTGCAGTTACACAATGTTATTCCGATATGGCTTCACGCCATCATTATCAA
AATTGAGAAAGTTGCAGCAATCAAGACTCGTCGTGCACACATCAAGCAATTCCACGATTC
AAAGATCAGATTCCCATTGGTGCAGCGATATCATCACAAACGCTATCGTCAACTGTTCTC
AATTGCTCGCCCAACTACACACTTCAACTAA

>g1710.t11 Gene=g1710 Length=121
MKAKGVLKEYEIIGRKLPSEKDPNPPLFKMIIFAPDHIVAKSRFWYFLRQLRKFKKATGE
IVSVKRKYEKTPLKIKNFGIWLRYDSRSGTHNMYREYRDLTIGGAVTQCYSDMASRHHYQ
N

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g1710.t11 Gene3D G3DSA:3.10.20.10 - 2 72 0.00000
7 g1710.t11 Gene3D G3DSA:3.10.20.10 - 73 121 0.00000
4 g1710.t11 Hamap MF_00273 50S ribosomal protein L18Ae [rpl18a]. 7 70 20.81907
2 g1710.t11 PANTHER PTHR10052:SF1 60S RIBOSOMAL PROTEIN L18A 5 119 0.00000
3 g1710.t11 PANTHER PTHR10052 60S RIBOSOMAL PROTEIN L18A 5 119 0.00000
1 g1710.t11 Pfam PF01775 Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A 7 120 0.00000
5 g1710.t11 SUPERFAMILY SSF160374 RplX-like 72 119 0.00000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005840 ribosome CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed