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.t19 TSS g12102.t19 20939009 20939009
chr_1 g12102 g12102.t19 isoform g12102.t19 20939077 20940413
chr_1 g12102 g12102.t19 exon g12102.t19.exon1 20939077 20939091
chr_1 g12102 g12102.t19 cds g12102.t19.CDS1 20939077 20939091
chr_1 g12102 g12102.t19 exon g12102.t19.exon2 20939358 20939631
chr_1 g12102 g12102.t19 cds g12102.t19.CDS2 20939358 20939631
chr_1 g12102 g12102.t19 exon g12102.t19.exon3 20939691 20939915
chr_1 g12102 g12102.t19 cds g12102.t19.CDS3 20939691 20939915
chr_1 g12102 g12102.t19 exon g12102.t19.exon4 20940127 20940413
chr_1 g12102 g12102.t19 cds g12102.t19.CDS4 20940127 20940413
chr_1 g12102 g12102.t19 TTS g12102.t19 20940505 20940505

Sequences

>g12102.t19 Gene=g12102 Length=801
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTA
TTTAAAGTTTTGGAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAG
AAAAAGGCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACA
TTGAGAGCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTT
GTCATCTCACATGACGTTGATCCAATCGAAGTGACCTTATGCCGTAAAATGGGAGTTCCA
TATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACA
ACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAA
TCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGT
TTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAA
TTAGCCCAAAAACAAGGATAA

>g12102.t19 Gene=g12102 Length=266
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLK
KKAEEKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIEVTLCRKMGVP
YCIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGG
LLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12102.t19 Gene3D G3DSA:3.30.1330.210 - 62 241 1.1E-83
2 g12102.t19 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 263 1.4E-99
3 g12102.t19 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 263 1.4E-99
8 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 1.6E-60
5 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 1.6E-60
7 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 1.6E-60
4 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 102 115 1.6E-60
11 g12102.t19 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 141 155 1.2E-7
10 g12102.t19 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 160 173 1.2E-7
6 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 193 217 1.6E-60
9 g12102.t19 PRINTS PR00882 Ribosomal protein L7A family signature 225 245 1.6E-60
1 g12102.t19 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 135 211 1.4E-17
13 g12102.t19 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 174 191 -
12 g12102.t19 SUPERFAMILY SSF55315 L30e-like 97 227 1.51E-28
14 g12102.t19 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

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. There were no conditions that were differentially expressed