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.t51 TSS g12102.t51 20939009 20939009
chr_1 g12102 g12102.t51 isoform g12102.t51 20939077 20940413
chr_1 g12102 g12102.t51 exon g12102.t51.exon1 20939077 20939091
chr_1 g12102 g12102.t51 cds g12102.t51.CDS1 20939077 20939091
chr_1 g12102 g12102.t51 exon g12102.t51.exon2 20939373 20939631
chr_1 g12102 g12102.t51 cds g12102.t51.CDS2 20939373 20939631
chr_1 g12102 g12102.t51 exon g12102.t51.exon3 20939691 20939911
chr_1 g12102 g12102.t51 cds g12102.t51.CDS3 20939691 20939911
chr_1 g12102 g12102.t51 exon g12102.t51.exon4 20940108 20940413
chr_1 g12102 g12102.t51 cds g12102.t51.CDS4 20940108 20940413
chr_1 g12102 g12102.t51 TTS g12102.t51 20940505 20940505

Sequences

>g12102.t51 Gene=g12102 Length=801
ATGGTCGCTAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCTCCTCTTTCAAAATCA
GCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGTCCCAAGAATTATGGT
ATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTTAGATGGCCAAAATAT
ATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAGGTTCCACCACCAATT
AATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTATTTAAAGTTTTGGAA
AAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAAGAA
AAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTGC
AACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGAC
GTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCCA
TATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACA
ACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAA
TCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGT
TTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAA
TTAGCCCAAAAACAAGGATAA

>g12102.t51 Gene=g12102 Length=266
MVAKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFVRWPKY
IRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLKKKAEE
KVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVP
YCIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGG
LLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12102.t51 Gene3D G3DSA:3.30.1330.210 - 57 241 9.1E-92
2 g12102.t51 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 7 263 9.9E-108
3 g12102.t51 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 7 263 9.9E-108
4 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 36 53 4.4E-70
8 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 53 70 4.4E-70
7 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 73 92 4.4E-70
5 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 97 110 4.4E-70
10 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 132 152 4.4E-70
14 g12102.t51 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 136 150 1.6E-23
12 g12102.t51 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 155 168 1.6E-23
11 g12102.t51 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 171 181 1.6E-23
13 g12102.t51 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 181 195 1.6E-23
6 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 193 217 4.4E-70
9 g12102.t51 PRINTS PR00882 Ribosomal protein L7A family signature 225 245 4.4E-70
1 g12102.t51 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 130 211 6.5E-23
16 g12102.t51 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 174 191 -
15 g12102.t51 SUPERFAMILY SSF55315 L30e-like 92 227 1.59E-33
17 g12102.t51 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 24 -

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