Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L7a.

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 g12102 g12102.t53 TSS g12102.t53 20939009 20939009
chr_1 g12102 g12102.t53 isoform g12102.t53 20939077 20940413
chr_1 g12102 g12102.t53 exon g12102.t53.exon1 20939077 20939091
chr_1 g12102 g12102.t53 cds g12102.t53.CDS1 20939077 20939091
chr_1 g12102 g12102.t53 exon g12102.t53.exon2 20939358 20939541
chr_1 g12102 g12102.t53 cds g12102.t53.CDS2 20939358 20939541
chr_1 g12102 g12102.t53 exon g12102.t53.exon3 20939730 20939911
chr_1 g12102 g12102.t53 cds g12102.t53.CDS3 20939730 20939911
chr_1 g12102 g12102.t53 exon g12102.t53.exon4 20940108 20940413
chr_1 g12102 g12102.t53 cds g12102.t53.CDS4 20940108 20940413
chr_1 g12102 g12102.t53 TTS g12102.t53 20940505 20940505

Sequences

>g12102.t53 Gene=g12102 Length=687
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCT
GAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCT
GGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCA
CATGACGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGA
GTTCCATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACA
TGCACAACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATC
GTGGAATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGT
GGTGGTTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCT
CGTGAATTAGCCCAAAAACAAGGATAA

>g12102.t53 Gene=g12102 Length=228
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIQSKLQKAARLKKKAEEKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVIS
HDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKI
VESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12102.t53 Gene3D G3DSA:3.30.1330.210 - 58 222 5.7E-70
17 g12102.t53 MobiDBLite mobidb-lite consensus disorder prediction 22 48 -
3 g12102.t53 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 77 1.7E-88
5 g12102.t53 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 77 1.7E-88
2 g12102.t53 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 71 225 1.7E-88
4 g12102.t53 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 71 225 1.7E-88
8 g12102.t53 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 4.1E-14
6 g12102.t53 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 4.1E-14
9 g12102.t53 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 98 112 9.9E-24
10 g12102.t53 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 117 130 9.9E-24
12 g12102.t53 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 133 143 9.9E-24
7 g12102.t53 PRINTS PR00882 Ribosomal protein L7A family signature 141 161 4.1E-14
11 g12102.t53 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 143 157 9.9E-24
1 g12102.t53 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 92 173 3.9E-23
16 g12102.t53 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 136 153 -
13 g12102.t53 SUPERFAMILY SSF55315 L30e-like 85 200 9.97E-32
14 g12102.t53 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -

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:0042254 ribosome biogenesis BP
GO:1990904 ribonucleoprotein complex CC

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