General information for g6187.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g6187 is located on chr_2: 15042422..15042979 (- 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_2 | g6187 | g6187.t1 | TTS | g6187.t1 | 15042359 | 15042359 |
| chr_2 | g6187 | g6187.t1 | isoform | g6187.t1 | 15042422 | 15042979 |
| chr_2 | g6187 | g6187.t1 | exon | g6187.t1.exon1 | 15042422 | 15042979 |
| chr_2 | g6187 | g6187.t1 | cds | g6187.t1.CDS1 | 15042422 | 15042979 |
| chr_2 | g6187 | g6187.t1 | TSS | g6187.t1 | 15043095 | 15043095 |
Sequences
>g6187.t1 Gene=g6187 Length=558
ATGTTGAAGTCAACAACAATGATCAATTTAATAAGAATCAGCTCGAGATCGATGAGAACT
TCAACAATTTATAGAAATGTTGAAGCCGCAACAGCATCAGCAGAGAAATTAACAATACCG
GTCCCTGAAGGAACAGAAAAACCAGCAAATCCAAAACTCAATAGCATTGTCGATCAAATT
GCAGGATTAAATTTATTAGAAGTCAGCGAATTGAGTAGTTTATTAAAGAAAAAATTGAAC
CTTCCTGACACAGCAATGATGATGCCATCGATGGGTAATTTTGCAGCAGCTCCTGCACAA
GCCGCCGCTGAGGAAGAAGAAGCCGCACCTAAAACCGTCAAGTCATCATTCAAAGTTAAA
ATGACCAAATTCGATGAGAAACAAAAAGTTGCATTGATTAAAGAAGTAAAGAACCTCTTT
GATGGAATGAATTTGGTACAAGCAAAGAAATTTGTCGAGAGTGTGCCGACAATTGTAAAA
GAGGATGTTTCAAAGGATGAGGCTGAGAAACTGAAAGAAACACTATCAAAGATTGGAGCT
ACAATTGAAATTGAGTAG
>g6187.t1 Gene=g6187 Length=185
MLKSTTMINLIRISSRSMRTSTIYRNVEAATASAEKLTIPVPEGTEKPANPKLNSIVDQI
AGLNLLEVSELSSLLKKKLNLPDTAMMMPSMGNFAAAPAQAAAEEEEAAPKTVKSSFKVK
MTKFDEKQKVALIKEVKNLFDGMNLVQAKKFVESVPTIVKEDVSKDEAEKLKETLSKIGA
TIEIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6187.t1 | CDD | cd00387 | Ribosomal_L7_L12 | 51 | 184 | 0.000000 |
| 8 | g6187.t1 | Gene3D | G3DSA:1.20.5.710 | Single helix bin | 52 | 108 | 0.000021 |
| 9 | g6187.t1 | Gene3D | G3DSA:3.30.1390.10 | - | 109 | 185 | 0.000000 |
| 5 | g6187.t1 | Hamap | MF_00368 | 50S ribosomal protein L7/L12 [rplL]. | 49 | 185 | 17.076532 |
| 3 | g6187.t1 | PANTHER | PTHR45987:SF4 | 39S RIBOSOMAL PROTEIN L12, MITOCHONDRIAL | 20 | 185 | 0.000000 |
| 4 | g6187.t1 | PANTHER | PTHR45987 | 39S RIBOSOMAL PROTEIN L12 | 20 | 185 | 0.000000 |
| 1 | g6187.t1 | Pfam | PF16320 | Ribosomal protein L7/L12 dimerisation domain | 53 | 102 | 0.000000 |
| 2 | g6187.t1 | Pfam | PF00542 | Ribosomal protein L7/L12 C-terminal domain | 117 | 185 | 0.000000 |
| 6 | g6187.t1 | SUPERFAMILY | SSF48300 | Ribosomal protein L7/12, oligomerisation (N-terminal) domain | 52 | 105 | 0.000000 |
| 7 | g6187.t1 | SUPERFAMILY | SSF54736 | ClpS-like | 117 | 185 | 0.000000 |
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:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
KEGG
Orthology
- This transcript has been annotated with K02935 (large subunit ribosomal protein L7/L12)
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.
