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.t40 TTS g14004.t40 33960516 33960516
chr_1 g14004 g14004.t40 isoform g14004.t40 33960643 33963795
chr_1 g14004 g14004.t40 exon g14004.t40.exon1 33960643 33960909
chr_1 g14004 g14004.t40 cds g14004.t40.CDS1 33960643 33960909
chr_1 g14004 g14004.t40 exon g14004.t40.exon2 33960971 33961163
chr_1 g14004 g14004.t40 cds g14004.t40.CDS2 33960971 33961163
chr_1 g14004 g14004.t40 exon g14004.t40.exon3 33961316 33961615
chr_1 g14004 g14004.t40 cds g14004.t40.CDS3 33961316 33961614
chr_1 g14004 g14004.t40 exon g14004.t40.exon4 33963749 33963795
chr_1 g14004 g14004.t40 TSS g14004.t40 NA NA

Sequences

>g14004.t40 Gene=g14004 Length=807
TCAGATATTATAAAACAAAATTTAAAAATCGATGTGTTTTGATGCATAATGGCTCCTACA
GCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTTCCTGAATCAAAGTTGAAAGAT
GGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTCCGTAAACGCATTATTCGATCG
AAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCTGAAAAATATACACGCACATAT
TTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCTGCCAAGAAAGCTGGAAATATT
TATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGTATTCGTGGTGTCAACAAAGTC
GCTCCAAAGGTAAAGAAGGTCTTGCAATTGCTTCGCTTGCGTCAAATCAACAATGCTACA
TTTGTTAAGTTGAATAAGGCCACACTCAATATGTTGAGAATTGCTCAACCTTATATCACT
TATGGATATCCAACTCTCAAAACAGTTCGTGATTTGATCTATAAGAGAGGTTTCGTTAAG
CACGGAGGTCGACGCATTCCAATCACTGACAACTTTGTGATTGAACGCAAATTGAAAAAA
GGATACAATATTCAGTGTGTTGAAGATATGGTATATCAAATCTACACATGCGGCCGAGTG
TTCAAACAGGTAAACAACTTCCTCTGGCCATTCAAACTTAACACACCAACTGGTGGCTGG
CGTAAAAAGAACAACCACTTTGTTGAAGGAGGAGATTTCGGTAATCGTGAAGATAAAATC
AATGAACTCGTTCAACGTATGGTTTAA

>g14004.t40 Gene=g14004 Length=252
MAPTAKTASKDKKLPAVPESKLKDGKRRLASRGKLILRKRIIRSKVALRRRQNLVRAEKY
TRTYLKLQKDVIEQARAAKKAGNIYIPAYPKVAFVIRIRGVNKVAPKVKKVLQLLRLRQI
NNATFVKLNKATLNMLRIAQPYITYGYPTLKTVRDLIYKRGFVKHGGRRIPITDNFVIER
KLKKGYNIQCVEDMVYQIYTCGRVFKQVNNFLWPFKLNTPTGGWRKKNNHFVEGGDFGNR
EDKINELVQRMV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14004.t40 CDD cd01657 Ribosomal_L7_archeal_euk 92 252 7.03771E-85
7 g14004.t40 Coils Coil Coil 244 252 -
5 g14004.t40 Gene3D G3DSA:3.30.1390.20 - 95 240 4.5E-30
6 g14004.t40 Gene3D G3DSA:1.10.15.30 - 149 212 4.5E-30
10 g14004.t40 MobiDBLite mobidb-lite consensus disorder prediction 1 23 -
3 g14004.t40 PANTHER PTHR11524 60S RIBOSOMAL PROTEIN L7 11 251 1.7E-83
2 g14004.t40 Pfam PF08079 Ribosomal L30 N-terminal domain 17 88 1.0E-11
1 g14004.t40 Pfam PF00327 Ribosomal protein L30p/L7e 93 143 6.3E-21
9 g14004.t40 ProSitePatterns PS00634 Ribosomal protein L30 signature. 111 143 -
4 g14004.t40 SUPERFAMILY SSF55129 Ribosomal protein L30p/L7e 93 252 4.58E-58
11 g14004.t40 TIGRFAM TIGR01310 uL30_euk: 60S ribosomal protein uL30 18 252 1.9E-87

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