Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t2 isoform g14071.t2 34478440 34479495
chr_1 g14071 g14071.t2 exon g14071.t2.exon1 34478440 34478603
chr_1 g14071 g14071.t2 exon g14071.t2.exon2 34478847 34479027
chr_1 g14071 g14071.t2 cds g14071.t2.CDS1 34478860 34479027
chr_1 g14071 g14071.t2 exon g14071.t2.exon3 34479211 34479495
chr_1 g14071 g14071.t2 cds g14071.t2.CDS2 34479211 34479495
chr_1 g14071 g14071.t2 TTS g14071.t2 34479591 34479591
chr_1 g14071 g14071.t2 TSS g14071.t2 NA NA

Sequences

>g14071.t2 Gene=g14071 Length=630
TTTTTTGCAGAAAATAACAAATTTTAGGAAAATCCGCGAAAAAATTCAGTTATAAATAAC
AGACAAAAGTTTCAAAAAACAGGGGTGTGAAGAAATTTTTATAAAAAATTCACAAGCCTA
ATTCTTTTCTCAGCGGAATTCTTTGATTCTACACGTTTTTAAAAGAAATTCCACAAAATG
AAGTTTAATAGAAACGTCTCATCATCGCGTCGCAAGAGTCGTCTTCGACATTTTACAGCT
CCATCGCATATTCGTAGAAAGATAATGTCATCACCATTGAGCAAAGAACTCAGACAAAAA
TATAATGTTCGCTCAATGCCAATTCGTAAAGATGATGAAGTTCAAGTCGTTCGTGGTCAC
TATAAAGGAAATCAAGTTGGCAAAGTAGTGCAAGTGTACAGAAAGAAATTTGTTGTGTAC
ATTGAACGAATCCAGCGCGAGAAGGCAAATGGAACTAATGTTTATGTTGGAATTCATCCA
TCAAAACTTTTGATTGTCAAACTCAAGATGGACAAAGACCGCAAACGCATCTTGGATCGC
AGAGCAAAGGGACGTTTGGCTGCTCTTGGAAAAGATAAGGGCAAATATACAGAAGAAACA
GCTGCTGCTCCAATGGAAACTACATCCTAA

>g14071.t2 Gene=g14071 Length=150
MKFNRNVSSSRRKSRLRHFTAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRG
HYKGNQVGKVVQVYRKKFVVYIERIQREKANGTNVYVGIHPSKLLIVKLKMDKDRKRILD
RRAKGRLAALGKDKGKYTEETAAAPMETTS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g14071.t2 CDD cd06089 KOW_RPL26 52 106 1.26967E-13
8 g14071.t2 Gene3D G3DSA:2.30.30.30 - 1 147 7.5E-63
5 g14071.t2 Hamap MF_01326_A 50S ribosomal protein L24 [rplX]. 9 122 20.841011
3 g14071.t2 PANTHER PTHR11143 60S RIBOSOMAL PROTEIN L26 FAMILY MEMBER 1 141 9.1E-78
4 g14071.t2 PANTHER PTHR11143:SF10 60S RIBOSOMAL PROTEIN L26-LIKE 1 1 141 9.1E-78
1 g14071.t2 Pfam PF16906 Ribosomal proteins L26 eukaryotic, L24P archaeal 8 122 1.9E-39
2 g14071.t2 Pfam PF00467 KOW motif 51 83 1.5E-7
10 g14071.t2 ProSitePatterns PS01108 Ribosomal protein L24 signature. 52 70 -
11 g14071.t2 SMART SM00739 kow_9 48 76 0.0026
6 g14071.t2 SUPERFAMILY SSF50104 Translation proteins SH3-like domain 8 126 2.56E-35
7 g14071.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 10 -
12 g14071.t2 TIGRFAM TIGR01080 rplX_A_E: ribosomal protein uL24 8 123 3.2E-46

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