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.t21 TSS g12102.t21 20939009 20939009
chr_1 g12102 g12102.t21 isoform g12102.t21 20939077 20940413
chr_1 g12102 g12102.t21 exon g12102.t21.exon1 20939077 20939099
chr_1 g12102 g12102.t21 cds g12102.t21.CDS1 20939077 20939099
chr_1 g12102 g12102.t21 exon g12102.t21.exon2 20939441 20939631
chr_1 g12102 g12102.t21 cds g12102.t21.CDS2 20939441 20939631
chr_1 g12102 g12102.t21 exon g12102.t21.exon3 20939691 20939911
chr_1 g12102 g12102.t21 cds g12102.t21.CDS3 20939691 20939911
chr_1 g12102 g12102.t21 exon g12102.t21.exon4 20940108 20940413
chr_1 g12102 g12102.t21 cds g12102.t21.CDS4 20940108 20940413
chr_1 g12102 g12102.t21 TTS g12102.t21 20940505 20940505

Sequences

>g12102.t21 Gene=g12102 Length=741
ATGGTCGCTAAAAAGGTTGGTTTCAATCCATTGTTCGAAAAACGTCCCAAGAATTATGGT
ATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTTAGATGGCCAAAATAT
ATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAGGTTCCACCACCAATT
AATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTATTTAAAGTTTTGGAA
AAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAAGAA
AAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTGC
AACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGAC
GTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCCA
TATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCACA
ACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGAA
TCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGGT
TTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGAA
TTAGCCCAAAAACAAGGATAA

>g12102.t21 Gene=g12102 Length=246
MVAKKVGFNPLFEKRPKNYGIGQNVQPKRDLSRFVRWPKYIRIQRHKAILQKRLKVPPPI
NQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLKKKAEEKVAGKDDAPSKKKLTLRAGC
NTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLVHRKTCT
TLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVEKAKARE
LAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g12102.t21 Gene3D G3DSA:3.30.1330.210 - 37 221 7.1E-92
2 g12102.t21 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 3 243 1.1E-105
3 g12102.t21 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 3 243 1.1E-105
8 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 16 33 2.9E-70
10 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 33 50 2.9E-70
7 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 53 72 2.9E-70
9 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 77 90 2.9E-70
6 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 112 132 2.9E-70
13 g12102.t21 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 116 130 1.3E-23
12 g12102.t21 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 135 148 1.3E-23
14 g12102.t21 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 151 161 1.3E-23
11 g12102.t21 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 161 175 1.3E-23
4 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 173 197 2.9E-70
5 g12102.t21 PRINTS PR00882 Ribosomal protein L7A family signature 205 225 2.9E-70
1 g12102.t21 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 110 191 5.7E-23
16 g12102.t21 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 154 171 -
15 g12102.t21 SUPERFAMILY SSF55315 L30e-like 72 207 1.29E-33

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