Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 60S ribosomal protein L26.

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_1 g14071 g14071.t14 TSS g14071.t14 34478846 34478846
chr_1 g14071 g14071.t14 isoform g14071.t14 34478860 34479495
chr_1 g14071 g14071.t14 exon g14071.t14.exon1 34478860 34478877
chr_1 g14071 g14071.t14 exon g14071.t14.exon2 34478921 34479027
chr_1 g14071 g14071.t14 cds g14071.t14.CDS1 34478947 34479027
chr_1 g14071 g14071.t14 exon g14071.t14.exon3 34479211 34479495
chr_1 g14071 g14071.t14 cds g14071.t14.CDS2 34479211 34479495
chr_1 g14071 g14071.t14 TTS g14071.t14 34479591 34479591

Sequences

>g14071.t14 Gene=g14071 Length=410
ATGAAGTTTAATAGAAACCTCCATCGCATATTCGTAGAAAGATAATGTCATCACCATTGA
GCAAAGAACTCAGACAAAAATATAATGTTCGCTCAATGCCAATTCGTAAAGATGATGAAG
TTCAAGTCGTTCGTGGTCACTATAAAGGAAATCAAGTTGGCAAAGTAGTGCAAGTGTACA
GAAAGAAATTTGTTGTGTACATTGAACGAATCCAGCGCGAGAAGGCAAATGGAACTAATG
TTTATGTTGGAATTCATCCATCAAAACTTTTGATTGTCAAACTCAAGATGGACAAAGACC
GCAAACGCATCTTGGATCGCAGAGCAAAGGGACGTTTGGCTGCTCTTGGAAAAGATAAGG
GCAAATATACAGAAGAAACAGCTGCTGCTCCAATGGAAACTACATCCTAA

>g14071.t14 Gene=g14071 Length=121
MSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGNQVGKVVQVYRKKFVVYIERIQREK
ANGTNVYVGIHPSKLLIVKLKMDKDRKRILDRRAKGRLAALGKDKGKYTEETAAAPMETT
S

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g14071.t14 CDD cd06089 KOW_RPL26 23 77 1.03148E-13
6 g14071.t14 Gene3D G3DSA:2.30.30.30 - 1 118 1.4E-49
3 g14071.t14 PANTHER PTHR11143 60S RIBOSOMAL PROTEIN L26 FAMILY MEMBER 1 112 3.5E-62
4 g14071.t14 PANTHER PTHR11143:SF10 60S RIBOSOMAL PROTEIN L26-LIKE 1 1 112 3.5E-62
1 g14071.t14 Pfam PF16906 Ribosomal proteins L26 eukaryotic, L24P archaeal 1 93 1.1E-27
2 g14071.t14 Pfam PF00467 KOW motif 22 54 1.0E-7
8 g14071.t14 ProSitePatterns PS01108 Ribosomal protein L24 signature. 23 41 -
9 g14071.t14 SMART SM00739 kow_9 19 47 0.0026
5 g14071.t14 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 1 97 5.64E-28
10 g14071.t14 TIGRFAM TIGR01080 rplX_A_E: ribosomal protein uL24 1 94 3.9E-37

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:0003723 RNA binding MF
GO:0015934 large ribosomal subunit CC
GO:0006412 translation BP
GO:0003735 structural constituent of ribosome MF

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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