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.t44 TTS g14004.t44 33960516 33960516
chr_1 g14004 g14004.t44 isoform g14004.t44 33960643 33963795
chr_1 g14004 g14004.t44 exon g14004.t44.exon1 33960643 33960909
chr_1 g14004 g14004.t44 cds g14004.t44.CDS1 33960643 33960909
chr_1 g14004 g14004.t44 exon g14004.t44.exon2 33960971 33961163
chr_1 g14004 g14004.t44 cds g14004.t44.CDS2 33960971 33961163
chr_1 g14004 g14004.t44 exon g14004.t44.exon3 33961316 33961615
chr_1 g14004 g14004.t44 cds g14004.t44.CDS3 33961316 33961615
chr_1 g14004 g14004.t44 exon g14004.t44.exon4 33963739 33963795
chr_1 g14004 g14004.t44 cds g14004.t44.CDS4 33963739 33963764
chr_1 g14004 g14004.t44 TSS g14004.t44 NA NA

Sequences

>g14004.t44 Gene=g14004 Length=817
TCAGATATTATAAAACAAAATTTAAAAATCGATGTGTTTTGATGCATGTCTCAATATAAT
GGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTTCCTGAATCAAA
GTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTCCGTAAACGCAT
TATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCTGAAAAATATAC
ACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCTGCCAAGAAAGC
TGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGTATTCGTGGTGT
CAACAAAGTCGCTCCAAAGGTAAAGAAGGTCTTGCAATTGCTTCGCTTGCGTCAAATCAA
CAATGCTACATTTGTTAAGTTGAATAAGGCCACACTCAATATGTTGAGAATTGCTCAACC
TTATATCACTTATGGATATCCAACTCTCAAAACAGTTCGTGATTTGATCTATAAGAGAGG
TTTCGTTAAGCACGGAGGTCGACGCATTCCAATCACTGACAACTTTGTGATTGAACGCAA
ATTGAAAAAAGGATACAATATTCAGTGTGTTGAAGATATGGTATATCAAATCTACACATG
CGGCCGAGTGTTCAAACAGGTAAACAACTTCCTCTGGCCATTCAAACTTAACACACCAAC
TGGTGGCTGGCGTAAAAAGAACAACCACTTTGTTGAAGGAGGAGATTTCGGTAATCGTGA
AGATAAAATCAATGAACTCGTTCAACGTATGGTTTAA

>g14004.t44 Gene=g14004 Length=261
MCFDACLNIMAPTAKTASKDKKLPAVPESKLKDGKRRLASRGKLILRKRIIRSKVALRRR
QNLVRAEKYTRTYLKLQKDVIEQARAAKKAGNIYIPAYPKVAFVIRIRGVNKVAPKVKKV
LQLLRLRQINNATFVKLNKATLNMLRIAQPYITYGYPTLKTVRDLIYKRGFVKHGGRRIP
ITDNFVIERKLKKGYNIQCVEDMVYQIYTCGRVFKQVNNFLWPFKLNTPTGGWRKKNNHF
VEGGDFGNREDKINELVQRMV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g14004.t44 CDD cd01657 Ribosomal_L7_archeal_euk 101 261 1.42566E-85
7 g14004.t44 Gene3D G3DSA:3.30.1390.20 - 104 249 5.0E-30
8 g14004.t44 Gene3D G3DSA:1.10.15.30 - 158 221 5.0E-30
3 g14004.t44 PANTHER PTHR11524:SF12 60S RIBOSOMAL PROTEIN L7 20 260 1.1E-83
4 g14004.t44 PANTHER PTHR11524 60S RIBOSOMAL PROTEIN L7 20 260 1.1E-83
2 g14004.t44 Pfam PF08079 Ribosomal L30 N-terminal domain 26 97 1.1E-11
1 g14004.t44 Pfam PF00327 Ribosomal protein L30p/L7e 102 152 6.7E-21
6 g14004.t44 ProSitePatterns PS00634 Ribosomal protein L30 signature. 120 152 -
5 g14004.t44 SUPERFAMILY SSF55129 Ribosomal protein L30p/L7e 102 261 5.1E-58
9 g14004.t44 TIGRFAM TIGR01310 uL30_euk: 60S ribosomal protein uL30 27 261 2.2E-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