General information for g14004.t42
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L7.
Parent gene
- The parent gene g14004 is located on chr_1: 33960971..33965851 (- strand)
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.t42 | TTS | g14004.t42 | 33960516 | 33960516 |
| chr_1 | g14004 | g14004.t42 | isoform | g14004.t42 | 33960643 | 33963795 |
| chr_1 | g14004 | g14004.t42 | exon | g14004.t42.exon1 | 33960643 | 33960909 |
| chr_1 | g14004 | g14004.t42 | cds | g14004.t42.CDS1 | 33960643 | 33960909 |
| chr_1 | g14004 | g14004.t42 | exon | g14004.t42.exon2 | 33960971 | 33961163 |
| chr_1 | g14004 | g14004.t42 | cds | g14004.t42.CDS2 | 33960971 | 33961163 |
| chr_1 | g14004 | g14004.t42 | exon | g14004.t42.exon3 | 33961316 | 33961657 |
| chr_1 | g14004 | g14004.t42 | cds | g14004.t42.CDS3 | 33961316 | 33961614 |
| chr_1 | g14004 | g14004.t42 | exon | g14004.t42.exon4 | 33963763 | 33963795 |
| chr_1 | g14004 | g14004.t42 | TSS | g14004.t42 | NA | NA |
Sequences
>g14004.t42 Gene=g14004 Length=835
TCAGATATTATAAAACAAAATTTAAAAATCGATCGAGAATTAGTGTATTTAATTAATTGA
AATTCGTTCTTCTAGAATGGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCC
TGCAGTTCCTGAATCAAAGTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATT
AATTCTCCGTAAACGCATTATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGT
TCGTGCTGAAAAATATACACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGC
TCGCGCTGCCAAGAAAGCTGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGT
CATCCGTATTCGTGGTGTCAACAAAGTCGCTCCAAAGGTAAAGAAGGTCTTGCAATTGCT
TCGCTTGCGTCAAATCAACAATGCTACATTTGTTAAGTTGAATAAGGCCACACTCAATAT
GTTGAGAATTGCTCAACCTTATATCACTTATGGATATCCAACTCTCAAAACAGTTCGTGA
TTTGATCTATAAGAGAGGTTTCGTTAAGCACGGAGGTCGACGCATTCCAATCACTGACAA
CTTTGTGATTGAACGCAAATTGAAAAAAGGATACAATATTCAGTGTGTTGAAGATATGGT
ATATCAAATCTACACATGCGGCCGAGTGTTCAAACAGGTAAACAACTTCCTCTGGCCATT
CAAACTTAACACACCAACTGGTGGCTGGCGTAAAAAGAACAACCACTTTGTTGAAGGAGG
AGATTTCGGTAATCGTGAAGATAAAATCAATGAACTCGTTCAACGTATGGTTTAA
>g14004.t42 Gene=g14004 Length=252
MAPTAKTASKDKKLPAVPESKLKDGKRRLASRGKLILRKRIIRSKVALRRRQNLVRAEKY
TRTYLKLQKDVIEQARAAKKAGNIYIPAYPKVAFVIRIRGVNKVAPKVKKVLQLLRLRQI
NNATFVKLNKATLNMLRIAQPYITYGYPTLKTVRDLIYKRGFVKHGGRRIPITDNFVIER
KLKKGYNIQCVEDMVYQIYTCGRVFKQVNNFLWPFKLNTPTGGWRKKNNHFVEGGDFGNR
EDKINELVQRMV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g14004.t42 | CDD | cd01657 | Ribosomal_L7_archeal_euk | 92 | 252 | 7.03771E-85 |
| 5 | g14004.t42 | Gene3D | G3DSA:3.30.1390.20 | - | 95 | 240 | 4.5E-30 |
| 6 | g14004.t42 | Gene3D | G3DSA:1.10.15.30 | - | 149 | 212 | 4.5E-30 |
| 9 | g14004.t42 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 23 | - |
| 3 | g14004.t42 | PANTHER | PTHR11524 | 60S RIBOSOMAL PROTEIN L7 | 11 | 251 | 1.7E-83 |
| 2 | g14004.t42 | Pfam | PF08079 | Ribosomal L30 N-terminal domain | 17 | 88 | 1.0E-11 |
| 1 | g14004.t42 | Pfam | PF00327 | Ribosomal protein L30p/L7e | 93 | 143 | 6.3E-21 |
| 8 | g14004.t42 | ProSitePatterns | PS00634 | Ribosomal protein L30 signature. | 111 | 143 | - |
| 4 | g14004.t42 | SUPERFAMILY | SSF55129 | Ribosomal protein L30p/L7e | 93 | 252 | 4.58E-58 |
| 10 | g14004.t42 | 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
- This transcript has been annotated with K02937 (large subunit ribosomal protein L7e)
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.
