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.t48 TSS g12102.t48 20939009 20939009
chr_1 g12102 g12102.t48 isoform g12102.t48 20939077 20940413
chr_1 g12102 g12102.t48 exon g12102.t48.exon1 20939077 20939091
chr_1 g12102 g12102.t48 cds g12102.t48.CDS1 20939077 20939091
chr_1 g12102 g12102.t48 exon g12102.t48.exon2 20939376 20939631
chr_1 g12102 g12102.t48 cds g12102.t48.CDS2 20939376 20939631
chr_1 g12102 g12102.t48 exon g12102.t48.exon3 20939691 20939911
chr_1 g12102 g12102.t48 cds g12102.t48.CDS3 20939691 20939911
chr_1 g12102 g12102.t48 exon g12102.t48.exon4 20940108 20940413
chr_1 g12102 g12102.t48 cds g12102.t48.CDS4 20940108 20940413
chr_1 g12102 g12102.t48 TTS g12102.t48 20940505 20940505

Sequences

>g12102.t48 Gene=g12102 Length=798
ATGGTCGCTAAAAAGGTTGTTGGTAAAAAAGTGGCTGCTGCTCCTCTTTCAAAATCAGCA
GTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGTCCCAAGAATTATGGTATT
GGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTTAGATGGCCAAAATATATT
CGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAGGTTCCACCACCAATTAAT
CAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTATTTAAAGTTTTGGAAAAA
TATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAAGAAAAG
GTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTGCAAC
ACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGACGTT
GATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCCATAT
TGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACAACT
TTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAATCA
ATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGTTTA
CTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAATTA
GCCCAAAAACAAGGATAA

>g12102.t48 Gene=g12102 Length=265
MVAKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFVRWPKYI
RIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLKKKAEEK
VAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVPY
CIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGGL
LGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12102.t48 Gene3D G3DSA:3.30.1330.210 - 56 240 9.0E-92
2 g12102.t48 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 6 262 7.3E-108
3 g12102.t48 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 6 262 7.3E-108
6 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 35 52 4.3E-70
8 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 52 69 4.3E-70
10 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 72 91 4.3E-70
4 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 96 109 4.3E-70
9 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 131 151 4.3E-70
14 g12102.t48 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 135 149 1.6E-23
13 g12102.t48 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 154 167 1.6E-23
12 g12102.t48 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 170 180 1.6E-23
11 g12102.t48 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 180 194 1.6E-23
5 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 192 216 4.3E-70
7 g12102.t48 PRINTS PR00882 Ribosomal protein L7A family signature 224 244 4.3E-70
1 g12102.t48 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 129 210 6.5E-23
16 g12102.t48 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 173 190 -
15 g12102.t48 SUPERFAMILY SSF55315 L30e-like 91 226 1.58E-33
17 g12102.t48 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 23 -

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

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