Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L12.

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 g10871 g10871.t6 isoform g10871.t6 12375267 12375957
chr_1 g10871 g10871.t6 exon g10871.t6.exon1 12375267 12375560
chr_1 g10871 g10871.t6 TTS g10871.t6 12375274 12375274
chr_1 g10871 g10871.t6 cds g10871.t6.CDS1 12375365 12375560
chr_1 g10871 g10871.t6 exon g10871.t6.exon2 12375628 12375957
chr_1 g10871 g10871.t6 cds g10871.t6.CDS2 12375628 12375923
chr_1 g10871 g10871.t6 TSS g10871.t6 12376347 12376347

Sequences

>g10871.t6 Gene=g10871 Length=624
ATTTATTTCTTATTTTAGTTAATAAAGCAACAAAATGCCACCAAAATTTGATCCAACAGA
AATCAAGCTCGTCTATTTGAGATGCGTTGGCGGCGAGGTTGGTGCAACATCCTCACTTGC
TCCTAAAATCGGTCCACTCGGTTTATCACCAAAAAAAGTTGGTGACGATATTGCAAAAGC
CACTGGTGACTGGAAAGGACTCAAGATCACAGTTTGTCTCACCATTCAAAATCGTCAGGC
CACTATCTCAGTCGTTCCATCAGCTGCTTCAATGATCATTAAGGCATTGAAAGAACCACC
AAGAGACAGAAAGAAGGTGAAAAACAGTAATGGTAACATCACCTTTGATGAAGTTATTAG
CATTGCTCGCGTAATGAGACCACGTTCAATGGCTAAGGACCTCTCTGGCACAATCAAAGA
AATTTTAGGTACAGCTCACAGTGTTGGATGCACAATTGATGGACGTGCACCACATGACAT
TATCGATGACGTTAATTCAGGAGCTATCGAATGTCCAGACTCTTAAATTTGTTCATTTTC
ATCAAAAACAATTCCTGAAAATAAAAAGCGCGATTTTCTTGAAATAAAGAAATTTAAATT
TTCCTGAAGATCATGTGAACAAAA

>g10871.t6 Gene=g10871 Length=163
MPPKFDPTEIKLVYLRCVGGEVGATSSLAPKIGPLGLSPKKVGDDIAKATGDWKGLKITV
CLTIQNRQATISVVPSAASMIIKALKEPPRDRKKVKNSNGNITFDEVISIARVMRPRSMA
KDLSGTIKEILGTAHSVGCTIDGRAPHDIIDDVNSGAIECPDS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10871.t6 CDD cd00349 Ribosomal_L11 13 141 7.86184E-50
8 g10871.t6 Gene3D G3DSA:3.30.1550.10 Ribosomal protein L11 1 80 1.9E-45
9 g10871.t6 Gene3D G3DSA:1.10.10.250 - 81 161 1.8E-39
5 g10871.t6 Hamap MF_00736 50S ribosomal protein L11 [rplK]. 9 143 14.764257
3 g10871.t6 PANTHER PTHR11661:SF21 60S RIBOSOMAL PROTEIN L12 1 163 9.2E-88
4 g10871.t6 PANTHER PTHR11661 60S RIBOSOMAL PROTEIN L12 1 163 9.2E-88
2 g10871.t6 Pfam PF03946 Ribosomal protein L11, N-terminal domain 9 69 8.6E-21
1 g10871.t6 Pfam PF00298 Ribosomal protein L11, RNA binding domain 74 141 2.3E-15
11 g10871.t6 ProSitePatterns PS00359 Ribosomal protein L11 signature. 128 143 -
12 g10871.t6 SMART SM00649 rl11c 13 142 3.2E-55
6 g10871.t6 SUPERFAMILY SSF54747 Ribosomal L11/L12e N-terminal domain 1 86 2.22E-31
7 g10871.t6 SUPERFAMILY SSF46906 Ribosomal protein L11, C-terminal domain 75 145 1.44E-18

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

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