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.t9 TTS g1710.t9 12637218 12637218
chr_3 g1710 g1710.t9 isoform g1710.t9 12637362 12638250
chr_3 g1710 g1710.t9 exon g1710.t9.exon1 12637362 12637520
chr_3 g1710 g1710.t9 cds g1710.t9.CDS1 12637507 12637520
chr_3 g1710 g1710.t9 exon g1710.t9.exon2 12637581 12637941
chr_3 g1710 g1710.t9 cds g1710.t9.CDS2 12637581 12637941
chr_3 g1710 g1710.t9 exon g1710.t9.exon3 12638233 12638250
chr_3 g1710 g1710.t9 cds g1710.t9.CDS3 12638233 12638250
chr_3 g1710 g1710.t9 TSS g1710.t9 12638284 12638284

Sequences

>g1710.t9 Gene=g1710 Length=538
ATGAAAGCAAAAGGAGTGCTCAAAGAATATGAGATCATTGGCCGCAAATTGCCAAGTGAA
AAGGATCCAAATCCACCTCTATTCAAAATGATAATCTTTGCACCGGATCACATCGTAGCC
AAGTCTCGTTTCTGGTATTTCTTGCGTCAATTGCGCAAATTCAAGAAGGCCACCGGTGAG
ATCGTGAGTGTTAAGCGCAAATATGAGAAAACTCCACTCAAGATCAAGAATTTCGGTATC
TGGCTTCGTTATGACTCGCGTTCAGGAACACATAACATGTATCGCGAATACCGTGATTTG
ACAATTGGTGGTGCAGTTACACAATGTTATTCCGATATGGCTTCACGCCATCGTGCTCGC
GCTCACTCAATTCAAGTGAATTATCAAAATTGAGAAAGTTGCAGCAATCAAGACTCGTCG
TGCACACATCAAGCAATTCCACGATTCAAAGATCAGATTCCCATTGGTGCAGCGATATCA
TCACAAACGCTATCGTCAACTGTTCTCAATTGCTCGCCCAACTACACACTTCAACTAA

>g1710.t9 Gene=g1710 Length=130
MKAKGVLKEYEIIGRKLPSEKDPNPPLFKMIIFAPDHIVAKSRFWYFLRQLRKFKKATGE
IVSVKRKYEKTPLKIKNFGIWLRYDSRSGTHNMYREYRDLTIGGAVTQCYSDMASRHRAR
AHSIQVNYQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g1710.t9 Gene3D G3DSA:3.10.20.10 - 2 72 0.00000
6 g1710.t9 Gene3D G3DSA:3.10.20.10 - 73 128 0.00000
4 g1710.t9 Hamap MF_00273 50S ribosomal protein L18Ae [rpl18a]. 7 70 20.81907
2 g1710.t9 PANTHER PTHR10052:SF1 60S RIBOSOMAL PROTEIN L18A 5 126 0.00000
3 g1710.t9 PANTHER PTHR10052 60S RIBOSOMAL PROTEIN L18A 5 126 0.00000
8 g1710.t9 PIRSF PIRSF002190 Ribosomal_L18a 1 128 0.00000
1 g1710.t9 Pfam PF01775 Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A 7 126 0.00000
5 g1710.t9 SUPERFAMILY SSF160374 RplX-like 72 126 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.

Raw TPM values