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.t8 TSS g12102.t8 20939009 20939009
chr_1 g12102 g12102.t8 isoform g12102.t8 20939077 20939911
chr_1 g12102 g12102.t8 exon g12102.t8.exon1 20939077 20939091
chr_1 g12102 g12102.t8 cds g12102.t8.CDS1 20939077 20939091
chr_1 g12102 g12102.t8 exon g12102.t8.exon2 20939358 20939631
chr_1 g12102 g12102.t8 cds g12102.t8.CDS2 20939358 20939631
chr_1 g12102 g12102.t8 exon g12102.t8.exon3 20939691 20939911
chr_1 g12102 g12102.t8 cds g12102.t8.CDS3 20939691 20939911
chr_1 g12102 g12102.t8 TTS g12102.t8 20940505 20940505

Sequences

>g12102.t8 Gene=g12102 Length=510
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTA
TTTAAAGTTTTGGAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAG
AAAAAGGCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACA
TTGAGAGCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTT
GTCATCTCACATGACGTTGATCCAATCGAA

>g12102.t8 Gene=g12102 Length=170
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLK
KKAEEKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12102.t8 Gene3D G3DSA:3.30.1330.210 - 62 170 1.2E-46
12 g12102.t8 MobiDBLite mobidb-lite consensus disorder prediction 23 50 -
13 g12102.t8 MobiDBLite mobidb-lite consensus disorder prediction 116 135 -
2 g12102.t8 PANTHER PTHR23105:SF134 - 12 170 5.2E-56
3 g12102.t8 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 170 5.2E-56
8 g12102.t8 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 8.2E-46
5 g12102.t8 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 8.2E-46
7 g12102.t8 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 8.2E-46
4 g12102.t8 PRINTS PR00882 Ribosomal protein L7A family signature 102 115 8.2E-46
6 g12102.t8 PRINTS PR00882 Ribosomal protein L7A family signature 137 157 8.2E-46
10 g12102.t8 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 141 155 2.2E-7
9 g12102.t8 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 160 170 2.2E-7
1 g12102.t8 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 135 170 2.3E-7
11 g12102.t8 SUPERFAMILY SSF55315 L30e-like 97 170 1.1E-12
14 g12102.t8 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

There are no GO annotations for this transcript.

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