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.t31 TSS g12102.t31 20939009 20939009
chr_1 g12102 g12102.t31 isoform g12102.t31 20939077 20940413
chr_1 g12102 g12102.t31 exon g12102.t31.exon1 20939077 20939079
chr_1 g12102 g12102.t31 cds g12102.t31.CDS1 20939077 20939079
chr_1 g12102 g12102.t31 exon g12102.t31.exon2 20939358 20939631
chr_1 g12102 g12102.t31 cds g12102.t31.CDS2 20939358 20939631
chr_1 g12102 g12102.t31 exon g12102.t31.exon3 20939691 20939911
chr_1 g12102 g12102.t31 cds g12102.t31.CDS3 20939691 20939911
chr_1 g12102 g12102.t31 exon g12102.t31.exon4 20940108 20940413
chr_1 g12102 g12102.t31 cds g12102.t31.CDS4 20940108 20940413
chr_1 g12102 g12102.t31 TTS g12102.t31 20940505 20940505

Sequences

>g12102.t31 Gene=g12102 Length=804
ATGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCTCCTCTTTCAAAA
TCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGTCCCAAGAATTAT
GGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTTAGATGGCCAAAA
TATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAGGTTCCACCACCA
ATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTATTTAAAGTTTTG
GAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAA
GAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGT
TGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACAT
GACGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTT
CCATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGC
ACAACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTG
GAATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGT
GGTTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGT
GAATTAGCCCAAAAACAAGGATAA

>g12102.t31 Gene=g12102 Length=267
MPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFVRWPK
YIRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLKKKAE
EKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGV
PYCIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGG
GLLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12102.t31 Gene3D G3DSA:3.30.1330.210 - 58 242 9.2E-92
2 g12102.t31 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 8 264 7.3E-108
3 g12102.t31 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 8 264 7.3E-108
5 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 37 54 4.5E-70
7 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 54 71 4.5E-70
10 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 74 93 4.5E-70
9 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 98 111 4.5E-70
8 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 133 153 4.5E-70
13 g12102.t31 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 137 151 1.6E-23
12 g12102.t31 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 156 169 1.6E-23
14 g12102.t31 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 172 182 1.6E-23
11 g12102.t31 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 182 196 1.6E-23
6 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 194 218 4.5E-70
4 g12102.t31 PRINTS PR00882 Ribosomal protein L7A family signature 226 246 4.5E-70
1 g12102.t31 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 131 212 6.6E-23
16 g12102.t31 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 175 192 -
15 g12102.t31 SUPERFAMILY SSF55315 L30e-like 93 228 1.61E-33
17 g12102.t31 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 25 -

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.

Raw TPM values