Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal protein L7.

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 g14004 g14004.t19 TTS g14004.t19 33960516 33960516
chr_1 g14004 g14004.t19 isoform g14004.t19 33960643 33961615
chr_1 g14004 g14004.t19 exon g14004.t19.exon1 33960643 33960909
chr_1 g14004 g14004.t19 cds g14004.t19.CDS1 33960643 33960909
chr_1 g14004 g14004.t19 exon g14004.t19.exon2 33960977 33961163
chr_1 g14004 g14004.t19 cds g14004.t19.CDS2 33960977 33961163
chr_1 g14004 g14004.t19 exon g14004.t19.exon3 33961316 33961615
chr_1 g14004 g14004.t19 cds g14004.t19.CDS3 33961316 33961614
chr_1 g14004 g14004.t19 TSS g14004.t19 33961727 33961727

Sequences

>g14004.t19 Gene=g14004 Length=754
AATGGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTTCCTGAATC
AAAGTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTCCGTAAACG
CATTATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCTGAAAAATA
TACACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCTGCCAAGAA
AGCTGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGTATTCGTGG
TGTCAACAAAGTCGCTCCAAAGGTAAAGAAGGTCTTGCAATTGCTTCGCTTGCGTCAAAT
CAACAATGCTACATTTGTTAAGTTGAATAAGGCCACACTCAATATGTTGAGAATTGCTCA
ACCTTATATCACTTATGGATATCCAACTCTCAAAACAGTTCGTGATTTGATCTATAAGAG
AGGTTTCCACGGAGGTCGACGCATTCCAATCACTGACAACTTTGTGATTGAACGCAAATT
GAAAAAAGGATACAATATTCAGTGTGTTGAAGATATGGTATATCAAATCTACACATGCGG
CCGAGTGTTCAAACAGGTAAACAACTTCCTCTGGCCATTCAAACTTAACACACCAACTGG
TGGCTGGCGTAAAAAGAACAACCACTTTGTTGAAGGAGGAGATTTCGGTAATCGTGAAGA
TAAAATCAATGAACTCGTTCAACGTATGGTTTAA

>g14004.t19 Gene=g14004 Length=250
MAPTAKTASKDKKLPAVPESKLKDGKRRLASRGKLILRKRIIRSKVALRRRQNLVRAEKY
TRTYLKLQKDVIEQARAAKKAGNIYIPAYPKVAFVIRIRGVNKVAPKVKKVLQLLRLRQI
NNATFVKLNKATLNMLRIAQPYITYGYPTLKTVRDLIYKRGFHGGRRIPITDNFVIERKL
KKGYNIQCVEDMVYQIYTCGRVFKQVNNFLWPFKLNTPTGGWRKKNNHFVEGGDFGNRED
KINELVQRMV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14004.t19 CDD cd01657 Ribosomal_L7_archeal_euk 92 250 2.24538E-82
6 g14004.t19 Gene3D G3DSA:3.30.1390.20 - 95 238 2.8E-30
7 g14004.t19 Gene3D G3DSA:1.10.15.30 - 149 210 2.8E-30
10 g14004.t19 MobiDBLite mobidb-lite consensus disorder prediction 1 22 -
3 g14004.t19 PANTHER PTHR11524:SF12 60S RIBOSOMAL PROTEIN L7 11 249 1.4E-81
4 g14004.t19 PANTHER PTHR11524 60S RIBOSOMAL PROTEIN L7 11 249 1.4E-81
2 g14004.t19 Pfam PF08079 Ribosomal L30 N-terminal domain 17 88 1.0E-11
1 g14004.t19 Pfam PF00327 Ribosomal protein L30p/L7e 93 143 6.2E-21
9 g14004.t19 ProSitePatterns PS00634 Ribosomal protein L30 signature. 111 143 -
5 g14004.t19 SUPERFAMILY SSF55129 Ribosomal protein L30p/L7e 93 250 1.31E-56
11 g14004.t19 TIGRFAM TIGR01310 uL30_euk: 60S ribosomal protein uL30 18 250 7.1E-85

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:0022625 cytosolic large ribosomal subunit CC
GO:0003735 structural constituent of ribosome MF
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) BP

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