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.t2 isoform g12102.t2 20936384 20940413
chr_1 g12102 g12102.t2 exon g12102.t2.exon1 20936384 20936389
chr_1 g12102 g12102.t2 exon g12102.t2.exon2 20939029 20939091
chr_1 g12102 g12102.t2 cds g12102.t2.CDS1 20939077 20939091
chr_1 g12102 g12102.t2 exon g12102.t2.exon3 20939358 20939631
chr_1 g12102 g12102.t2 cds g12102.t2.CDS2 20939358 20939631
chr_1 g12102 g12102.t2 exon g12102.t2.exon4 20939691 20939911
chr_1 g12102 g12102.t2 cds g12102.t2.CDS3 20939691 20939911
chr_1 g12102 g12102.t2 exon g12102.t2.exon5 20940108 20940413
chr_1 g12102 g12102.t2 cds g12102.t2.CDS4 20940108 20940413
chr_1 g12102 g12102.t2 TTS g12102.t2 20940505 20940505
chr_1 g12102 g12102.t2 TSS g12102.t2 NA NA

Sequences

>g12102.t2 Gene=g12102 Length=870
AATTGAAATTGACGAAAACATCTCCGCAAAAAATAACGTGGAAAATATATCAAAATGGTC
GCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCTCCTCTT
TCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGTCCCAAG
AATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTTAGATGG
CCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAGGTTCCA
CCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGCCGTTCAATTATTTAAA
GTTTTGGAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAG
GCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGA
GCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATC
TCACATGACGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATG
GGAGTTCCATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAA
ACATGCACAACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAG
ATCGTGGAATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGG
GGTGGTGGTTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAA
GCTCGTGAATTAGCCCAAAAACAAGGATAA

>g12102.t2 Gene=g12102 Length=271
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTAVQLFKVLEKYRPESKLQKAARLK
KKAEEKVAGKDDAPSKKKLTLRAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCR
KMGVPYCIVKGKSRLGRLVHRKTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRR
HWGGGLLGPKSMARIAKVEKAKARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12102.t2 Gene3D G3DSA:3.30.1330.210 - 62 246 9.7E-92
2 g12102.t2 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 268 6.0E-108
3 g12102.t2 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 268 6.0E-108
10 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 4.9E-70
5 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 4.9E-70
9 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 78 97 4.9E-70
4 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 102 115 4.9E-70
7 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 137 157 4.9E-70
13 g12102.t2 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 141 155 1.7E-23
12 g12102.t2 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 160 173 1.7E-23
11 g12102.t2 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 176 186 1.7E-23
14 g12102.t2 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 186 200 1.7E-23
6 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 198 222 4.9E-70
8 g12102.t2 PRINTS PR00882 Ribosomal protein L7A family signature 230 250 4.9E-70
1 g12102.t2 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 135 216 6.9E-23
16 g12102.t2 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 179 196 -
15 g12102.t2 SUPERFAMILY SSF55315 L30e-like 97 232 1.67E-33
17 g12102.t2 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.

Raw TPM values