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.t49 TSS g12102.t49 20939009 20939009
chr_1 g12102 g12102.t49 isoform g12102.t49 20939077 20940413
chr_1 g12102 g12102.t49 exon g12102.t49.exon1 20939077 20939091
chr_1 g12102 g12102.t49 cds g12102.t49.CDS1 20939077 20939091
chr_1 g12102 g12102.t49 exon g12102.t49.exon2 20939358 20939631
chr_1 g12102 g12102.t49 cds g12102.t49.CDS2 20939358 20939631
chr_1 g12102 g12102.t49 exon g12102.t49.exon3 20939748 20939911
chr_1 g12102 g12102.t49 cds g12102.t49.CDS3 20939748 20939911
chr_1 g12102 g12102.t49 exon g12102.t49.exon4 20940108 20940413
chr_1 g12102 g12102.t49 cds g12102.t49.CDS4 20940108 20940413
chr_1 g12102 g12102.t49 TTS g12102.t49 20940505 20940505

Sequences

>g12102.t49 Gene=g12102 Length=759
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCTGCTCGTTTG
AAGAAAAAGGCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTG
ACATTGAGAGCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTA
GTTGTCATCTCACATGACGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGC
CGTAAAATGGGAGTTCCATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTT
CATCGCAAAACATGCACAACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAAC
TTCTCAAAGATCGTGGAATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGT
CGTCATTGGGGTGGTGGTTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAA
AAGGCTAAAGCTCGTGAATTAGCCCAAAAACAAGGATAA

>g12102.t49 Gene=g12102 Length=252
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTAARLKKKAEEKVAGKDDAPSKKKL
TLRAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLV
HRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVE
KAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g12102.t49 Gene3D G3DSA:3.30.1330.210 - 62 227 1.6E-76
2 g12102.t49 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 249 2.1E-100
3 g12102.t49 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 249 2.1E-100
6 g12102.t49 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 3.6E-29
4 g12102.t49 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 3.6E-29
5 g12102.t49 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 3.6E-29
10 g12102.t49 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 122 136 1.4E-23
8 g12102.t49 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 141 154 1.4E-23
9 g12102.t49 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 157 167 1.4E-23
7 g12102.t49 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 167 181 1.4E-23
1 g12102.t49 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 116 197 4.9E-23
12 g12102.t49 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 160 177 -
11 g12102.t49 SUPERFAMILY SSF55315 L30e-like 100 224 9.24E-32
13 g12102.t49 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