General information for g14004.t16
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.t16 | TTS | g14004.t16 | 33960516 | 33960516 |
| chr_1 | g14004 | g14004.t16 | isoform | g14004.t16 | 33960643 | 33961614 |
| chr_1 | g14004 | g14004.t16 | exon | g14004.t16.exon1 | 33960643 | 33960834 |
| chr_1 | g14004 | g14004.t16 | exon | g14004.t16.exon2 | 33960933 | 33961163 |
| chr_1 | g14004 | g14004.t16 | cds | g14004.t16.CDS1 | 33960956 | 33961163 |
| chr_1 | g14004 | g14004.t16 | exon | g14004.t16.exon3 | 33961316 | 33961614 |
| chr_1 | g14004 | g14004.t16 | cds | g14004.t16.CDS2 | 33961316 | 33961614 |
| chr_1 | g14004 | g14004.t16 | TSS | g14004.t16 | 33961727 | 33961727 |
Sequences
>g14004.t16 Gene=g14004 Length=722
ATGGCTCCTACAGCTAAAACGGCTTCAAAGGATAAGAAACTGCCTGCAGTTCCTGAATCA
AAGTTGAAAGATGGAAAACGTCGATTGGCATCTCGCGGAAAATTAATTCTCCGTAAACGC
ATTATTCGATCGAAAGTTGCTCTTCGCCGTCGTCAAAATCTCGTTCGTGCTGAAAAATAT
ACACGCACATATTTGAAATTGCAAAAGGATGTCATTGAGCAGGCTCGCGCTGCCAAGAAA
GCTGGAAATATTTATATCCCAGCATACCCGAAAGTTGCTTTTGTCATCCGTATTCGTGGT
GTCAACAAAGTCGCTCCAAAGGTAAAGAAGGTCTTGCAATTGCTTCGCTTGCGTCAAATC
AACAATGCTACATTTGTTAAGTTGAATAAGGCCACACTCAATATGTTGAGAATTGCTCAA
CCTTATATCACTTATGGATATCCAACTCTCAAAACAGTTCGTGATTTGATCTATAAGAGA
GGTTTCGTTAAGGTAAGCTTTATATGAGAATCAATTGTGGACATTATGTTTGTGTTGAAG
ATATGGTATATCAAATCTACACATGCGGCCGAGTGTTCAAACAGGTAAACAACTTCCTCT
GGCCATTCAAACTTAACACACCAACTGGTGGCTGGCGTAAAAAGAACAACCACTTTGTTG
AAGGAGGAGATTTCGGTAATCGTGAAGATAAAATCAATGAACTCGTTCAACGTATGGTTT
AA
>g14004.t16 Gene=g14004 Length=168
MAPTAKTASKDKKLPAVPESKLKDGKRRLASRGKLILRKRIIRSKVALRRRQNLVRAEKY
TRTYLKLQKDVIEQARAAKKAGNIYIPAYPKVAFVIRIRGVNKVAPKVKKVLQLLRLRQI
NNATFVKLNKATLNMLRIAQPYITYGYPTLKTVRDLIYKRGFVKVSFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g14004.t16 | CDD | cd01657 | Ribosomal_L7_archeal_euk | 92 | 165 | 1.21279E-37 |
| 8 | g14004.t16 | Gene3D | G3DSA:3.30.1390.20 | - | 92 | 166 | 2.9E-11 |
| 7 | g14004.t16 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 3 | g14004.t16 | PANTHER | PTHR11524:SF12 | 60S RIBOSOMAL PROTEIN L7 | 11 | 165 | 9.2E-45 |
| 4 | g14004.t16 | PANTHER | PTHR11524 | 60S RIBOSOMAL PROTEIN L7 | 11 | 165 | 9.2E-45 |
| 2 | g14004.t16 | Pfam | PF08079 | Ribosomal L30 N-terminal domain | 17 | 88 | 4.3E-12 |
| 1 | g14004.t16 | Pfam | PF00327 | Ribosomal protein L30p/L7e | 93 | 143 | 3.0E-21 |
| 6 | g14004.t16 | ProSitePatterns | PS00634 | Ribosomal protein L30 signature. | 111 | 143 | - |
| 5 | g14004.t16 | SUPERFAMILY | SSF55129 | Ribosomal protein L30p/L7e | 93 | 165 | 1.57E-27 |
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.
