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.t60 TSS g12102.t60 20939009 20939009
chr_1 g12102 g12102.t60 isoform g12102.t60 20939077 20940413
chr_1 g12102 g12102.t60 exon g12102.t60.exon1 20939077 20939091
chr_1 g12102 g12102.t60 cds g12102.t60.CDS1 20939077 20939091
chr_1 g12102 g12102.t60 exon g12102.t60.exon2 20939358 20939631
chr_1 g12102 g12102.t60 cds g12102.t60.CDS2 20939358 20939631
chr_1 g12102 g12102.t60 exon g12102.t60.exon3 20939787 20939911
chr_1 g12102 g12102.t60 cds g12102.t60.CDS3 20939787 20939911
chr_1 g12102 g12102.t60 exon g12102.t60.exon4 20940108 20940413
chr_1 g12102 g12102.t60 cds g12102.t60.CDS4 20940108 20940413
chr_1 g12102 g12102.t60 TTS g12102.t60 20940505 20940505

Sequences

>g12102.t60 Gene=g12102 Length=720
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGGCAAGGATGAT
GCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTGCAACACAGTCACCAAGTTGGTT
GAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGACGTTGATCCAATCGAATTGGTT
CTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCCATATTGCATCGTAAAGGGCAAA
TCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACAACTTTAGCTTTGTGCAATGTT
GATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAATCAATTAAGACCAACTATAAT
GATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGTTTACTCGGACCAAAATCAATG
GCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAATTAGCCCAAAAACAAGGATAA

>g12102.t60 Gene=g12102 Length=239
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTGKDDAPSKKKLTLRAGCNTVTKLV
EQKKAQLVVISHDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLVHRKTCTTLALCNV
DNADRANFSKIVESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12102.t60 Gene3D G3DSA:3.30.1330.210 - 62 97 1.0E-13
16 g12102.t60 Gene3D G3DSA:3.30.1330.210 - 98 214 2.7E-58
3 g12102.t60 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 97 4.4E-96
5 g12102.t60 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 97 4.4E-96
2 g12102.t60 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 94 236 4.4E-96
4 g12102.t60 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 94 236 4.4E-96
8 g12102.t60 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 1.7E-28
6 g12102.t60 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 1.7E-28
7 g12102.t60 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 1.7E-28
11 g12102.t60 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 109 123 1.1E-23
10 g12102.t60 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 128 141 1.1E-23
12 g12102.t60 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 144 154 1.1E-23
9 g12102.t60 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 154 168 1.1E-23
1 g12102.t60 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 103 184 4.5E-23
14 g12102.t60 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 147 164 -
13 g12102.t60 SUPERFAMILY SSF55315 L30e-like 100 211 1.23E-31
15 g12102.t60 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