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.t55 TSS g12102.t55 20939009 20939009
chr_1 g12102 g12102.t55 isoform g12102.t55 20939077 20940413
chr_1 g12102 g12102.t55 exon g12102.t55.exon1 20939077 20939095
chr_1 g12102 g12102.t55 cds g12102.t55.CDS1 20939077 20939095
chr_1 g12102 g12102.t55 exon g12102.t55.exon2 20939362 20939568
chr_1 g12102 g12102.t55 cds g12102.t55.CDS2 20939362 20939568
chr_1 g12102 g12102.t55 exon g12102.t55.exon3 20939691 20939911
chr_1 g12102 g12102.t55 cds g12102.t55.CDS3 20939691 20939911
chr_1 g12102 g12102.t55 exon g12102.t55.exon4 20940108 20940413
chr_1 g12102 g12102.t55 cds g12102.t55.CDS4 20940108 20940413
chr_1 g12102 g12102.t55 TTS g12102.t55 20940505 20940505

Sequences

>g12102.t55 Gene=g12102 Length=753
ATGGTCGCTAAAAAGGTTGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCCCGTTCAATTATTT
AAAGTTTTGGAAAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAA
AAGGCTGAAGAAAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTG
AGAGCTGGTTGCAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTC
ATCTCACATGACGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAA
ATGGGAGTTCCATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGC
AAAACATGCACAACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCA
AAGATCGTGGAATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCAT
TGGGGTGGTGGTTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCT
AAAGCTCGTGAATTAGCCCAAAAACAAGGATAA

>g12102.t55 Gene=g12102 Length=250
MVAKKVVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILPVQLFKVLEKYRPESKLQKAARLKKKAEEKVAGKDDAPSKKKLTL
RAGCNTVTKLVEQKKAQLVVISHDVDPIELVLFLPALCRKMGVPYCIVKGKSRLGRLVHR
KTCTTLALCNVDNADRANFSKIVESIKTNYNDRYDEIRRHWGGGLLGPKSMARIAKVEKA
KARELAQKQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12102.t55 Gene3D G3DSA:3.30.1330.210 - 74 244 6.7E-77
2 g12102.t55 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 12 79 1.3E-92
4 g12102.t55 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 12 79 1.3E-92
3 g12102.t55 PANTHER PTHR23105:SF159 60S RIBOSOMAL PROTEIN L7A 86 247 1.3E-92
5 g12102.t55 PANTHER PTHR23105 RIBOSOMAL PROTEIN L7AE FAMILY MEMBER 86 247 1.3E-92
7 g12102.t55 PRINTS PR00882 Ribosomal protein L7A family signature 41 58 2.3E-16
6 g12102.t55 PRINTS PR00882 Ribosomal protein L7A family signature 58 75 2.3E-16
11 g12102.t55 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 120 134 1.3E-23
10 g12102.t55 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 139 152 1.3E-23
8 g12102.t55 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 155 165 1.3E-23
9 g12102.t55 PRINTS PR00881 Ribosomal protein L7A/RS6 family signature 165 179 1.3E-23
1 g12102.t55 Pfam PF01248 Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 114 195 4.8E-23
13 g12102.t55 ProSitePatterns PS01082 Ribosomal protein L7Ae signature. 158 175 -
12 g12102.t55 SUPERFAMILY SSF55315 L30e-like 79 222 1.99E-33
14 g12102.t55 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

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. There were no conditions that were differentially expressed