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.t57 TSS g12102.t57 20939009 20939009
chr_1 g12102 g12102.t57 isoform g12102.t57 20939077 20940413
chr_1 g12102 g12102.t57 exon g12102.t57.exon1 20939077 20939091
chr_1 g12102 g12102.t57 cds g12102.t57.CDS1 20939077 20939091
chr_1 g12102 g12102.t57 exon g12102.t57.exon2 20939358 20939541
chr_1 g12102 g12102.t57 cds g12102.t57.CDS2 20939358 20939541
chr_1 g12102 g12102.t57 exon g12102.t57.exon3 20939691 20939911
chr_1 g12102 g12102.t57 cds g12102.t57.CDS3 20939691 20939911
chr_1 g12102 g12102.t57 exon g12102.t57.exon4 20940108 20940413
chr_1 g12102 g12102.t57 cds g12102.t57.CDS4 20940108 20940413
chr_1 g12102 g12102.t57 TTS g12102.t57 20940505 20940505

Sequences

>g12102.t57 Gene=g12102 Length=726
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCCCGTTCAATTATTTAAAGTTTTGGAAAAATATCGTCCAGAA
TCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAAGAAAAGGTTGCAGGCAAG
GATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTGCAACACAGTCACCAAG
TTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGACGTTGATCCAATCGAA
TTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCCATATTGCATCGTAAAG
GGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACAACTTTAGCTTTGTGC
AATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAATCAATTAAGACCAAC
TATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGTTTACTCGGACCAAAA
TCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAATTAGCCCAAAAACAA
GGATAA

>g12102.t57 Gene=g12102 Length=241
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIPVQLFKVLEKYRPESKLQKAARLKKKAEEKVAGKDDAPSKKKLTLRAGCNTVTK
LVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLVHRKTCTTLALC
NVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVEKAKARELAQKQ
G

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12102.t57 Gene3D G3DSA:3.30.1330.210 - 64 235 7.8E-77
16 g12102.t57 MobiDBLite mobidb-lite consensus disorder prediction 23 44 -
3 g12102.t57 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 70 8.9E-89
5 g12102.t57 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 70 8.9E-89
2 g12102.t57 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 79 238 8.9E-89
4 g12102.t57 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 79 238 8.9E-89
7 g12102.t57 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 5.0E-12
6 g12102.t57 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 5.0E-12
9 g12102.t57 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 111 125 1.2E-23
11 g12102.t57 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 130 143 1.2E-23
8 g12102.t57 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 146 156 1.2E-23
10 g12102.t57 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 156 170 1.2E-23
1 g12102.t57 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 105 186 4.5E-23
15 g12102.t57 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 149 166 -
12 g12102.t57 SUPERFAMILY SSF55315 L30e-like 70 213 1.72E-33
13 g12102.t57 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. There were no conditions that were differentially expressed