General information for g14004.t2
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.t2 | isoform | g14004.t2 | 33959597 | 33961614 |
| chr_1 | g14004 | g14004.t2 | exon | g14004.t2.exon1 | 33959597 | 33959723 |
| chr_1 | g14004 | g14004.t2 | exon | g14004.t2.exon2 | 33960524 | 33960909 |
| chr_1 | g14004 | g14004.t2 | cds | g14004.t2.CDS1 | 33960643 | 33960909 |
| chr_1 | g14004 | g14004.t2 | exon | g14004.t2.exon3 | 33960971 | 33961614 |
| chr_1 | g14004 | g14004.t2 | cds | g14004.t2.CDS2 | 33960971 | 33961192 |
| chr_1 | g14004 | g14004.t2 | TSS | g14004.t2 | 33961727 | 33961727 |
| chr_1 | g14004 | g14004.t2 | TTS | g14004.t2 | NA | NA |
Sequences
>g14004.t2 Gene=g14004 Length=1157
ATGGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTTCCTGAATCA
AAGTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTCCGTAAACGC
ATTATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCTGAAAAATAT
ACACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCTGCCAAGAAA
GCTGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGTATTCGTGGG
TGAGTATAATTATTTATATATAAAAGTGATAATAATTTTATTGATAAAATGATAGGATTT
AAACAATTCAATCAAAACAACGATAAAATTTTAATATTTATTTTAGTGAATTTTATAAGG
TTATGTTTTTATTTTATTCTTTTCTTTTTAGTGTCAACAAAGTCGCTCCAAAGGTAAAGA
AGGTCTTGCAATTGCTTCGCTTGCGTCAAATCAACAATGCTACATTTGTTAAGTTGAATA
AGGCCACACTCAATATGTTGAGAATTGCTCAACCTTATATCACTTATGGATATCCAACTC
TCAAAACAGTTCGTGATTTGATCTATAAGAGAGGTTTCGTTAAGCACGGAGGTCGACGCA
TTCCAATCACTGACAACTTTGTGATTGAACGCAAATTGAAAAAAGGATACAATATTCAGT
GTGTTGAAGATATGGTATATCAAATCTACACATGCGGCCGAGTGTTCAAACAGGTAAACA
ACTTCCTCTGGCCATTCAAACTTAACACACCAACTGGTGGCTGGCGTAAAAAGAACAACC
ACTTTGTTGAAGGAGGAGATTTCGGTAATCGTGAAGATAAAATCAATGAACTCGTTCAAC
GTATGGTTTAAGCCGATATATTCCATCTTCATAATTCAACTTTGATAAACATTCAATATA
ACAGCAGTTAAAACCAAGTGTGTGTGTAAGATTTAAACACATAAATAAAAGAAAGAATGT
GAATTATTACTCTGCTTTTCTTCACTATAATTTAACAGCTTTTCATTCAACTTTCTTAAA
TTTGCAATTTGTGCTTGATATGCTTCTTCTTGTTGTTTCCATTGTTCTTCTTGTGTTAAA
TTATTAGATTCTGCCAT
>g14004.t2 Gene=g14004 Length=162
MFLFYSFLFSVNKVAPKVKKVLQLLRLRQINNATFVKLNKATLNMLRIAQPYITYGYPTL
KTVRDLIYKRGFVKHGGRRIPITDNFVIERKLKKGYNIQCVEDMVYQIYTCGRVFKQVNN
FLWPFKLNTPTGGWRKKNNHFVEGGDFGNREDKINELVQRMV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g14004.t2 | CDD | cd01657 | Ribosomal_L7_archeal_euk | 11 | 162 | 2.77366E-81 |
| 5 | g14004.t2 | Gene3D | G3DSA:3.30.1390.20 | - | 12 | 150 | 1.4E-26 |
| 6 | g14004.t2 | Gene3D | G3DSA:1.10.15.30 | - | 59 | 122 | 1.4E-26 |
| 2 | g14004.t2 | PANTHER | PTHR11524 | 60S RIBOSOMAL PROTEIN L7 | 11 | 161 | 1.0E-66 |
| 1 | g14004.t2 | Pfam | PF00327 | Ribosomal protein L30p/L7e | 10 | 53 | 4.0E-16 |
| 8 | g14004.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 9 | g14004.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 10 | g14004.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 11 | g14004.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 7 | g14004.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 162 | - |
| 4 | g14004.t2 | ProSitePatterns | PS00634 | Ribosomal protein L30 signature. | 21 | 53 | - |
| 3 | g14004.t2 | SUPERFAMILY | SSF55129 | Ribosomal protein L30p/L7e | 10 | 162 | 1.44E-54 |
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.
