General information for g14004.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t28 | TTS | g14004.t28 | 33960516 | 33960516 |
| chr_1 | g14004 | g14004.t28 | isoform | g14004.t28 | 33960643 | 33961711 |
| chr_1 | g14004 | g14004.t28 | exon | g14004.t28.exon1 | 33960643 | 33960909 |
| chr_1 | g14004 | g14004.t28 | cds | g14004.t28.CDS1 | 33960643 | 33960909 |
| chr_1 | g14004 | g14004.t28 | exon | g14004.t28.exon2 | 33960971 | 33961163 |
| chr_1 | g14004 | g14004.t28 | cds | g14004.t28.CDS2 | 33960971 | 33961060 |
| chr_1 | g14004 | g14004.t28 | exon | g14004.t28.exon3 | 33961320 | 33961615 |
| chr_1 | g14004 | g14004.t28 | exon | g14004.t28.exon4 | 33961704 | 33961711 |
| chr_1 | g14004 | g14004.t28 | TSS | g14004.t28 | 33961727 | 33961727 |
Sequences
>g14004.t28 Gene=g14004 Length=764
TTCAAAACAATGGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTT
CCTGAATCAAAGTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTC
CGTAAACGCATTATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCT
GAAAAATATACACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCT
GCCAAGAAAGCTGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGT
ATTCTGTCAACAAAGTCGCTCCAAAGGTAAAGAAGGTCTTGCAATTGCTTCGCTTGCGTC
AAATCAACAATGCTACATTTGTTAAGTTGAATAAGGCCACACTCAATATGTTGAGAATTG
CTCAACCTTATATCACTTATGGATATCCAACTCTCAAAACAGTTCGTGATTTGATCTATA
AGAGAGGTTTCGTTAAGCACGGAGGTCGACGCATTCCAATCACTGACAACTTTGTGATTG
AACGCAAATTGAAAAAAGGATACAATATTCAGTGTGTTGAAGATATGGTATATCAAATCT
ACACATGCGGCCGAGTGTTCAAACAGGTAAACAACTTCCTCTGGCCATTCAAACTTAACA
CACCAACTGGTGGCTGGCGTAAAAAGAACAACCACTTTGTTGAAGGAGGAGATTTCGGTA
ATCGTGAAGATAAAATCAATGAACTCGTTCAACGTATGGTTTAA
>g14004.t28 Gene=g14004 Length=118
MLRIAQPYITYGYPTLKTVRDLIYKRGFVKHGGRRIPITDNFVIERKLKKGYNIQCVEDM
VYQIYTCGRVFKQVNNFLWPFKLNTPTGGWRKKNNHFVEGGDFGNREDKINELVQRMV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g14004.t28 | CDD | cd01657 | Ribosomal_L7_archeal_euk | 1 | 118 | 0.0e+00 |
| 3 | g14004.t28 | Gene3D | G3DSA:3.30.1390.20 | - | 41 | 118 | 8.1e-06 |
| 1 | g14004.t28 | PANTHER | PTHR11524 | 60S RIBOSOMAL PROTEIN L7 | 1 | 117 | 0.0e+00 |
| 2 | g14004.t28 | SUPERFAMILY | SSF55129 | Ribosomal protein L30p/L7e | 1 | 118 | 0.0e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
