General information for g12102.t28
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 60S ribosomal protein L7a.
Parent gene
- The parent gene g12102 is located on chr_1: 20940128..20940500 (+ 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 | g12102 | g12102.t28 | TSS | g12102.t28 | 20939009 | 20939009 |
| chr_1 | g12102 | g12102.t28 | isoform | g12102.t28 | 20939077 | 20940413 |
| chr_1 | g12102 | g12102.t28 | exon | g12102.t28.exon1 | 20939077 | 20939091 |
| chr_1 | g12102 | g12102.t28 | cds | g12102.t28.CDS1 | 20939077 | 20939091 |
| chr_1 | g12102 | g12102.t28 | exon | g12102.t28.exon2 | 20939358 | 20939635 |
| chr_1 | g12102 | g12102.t28 | cds | g12102.t28.CDS2 | 20939358 | 20939635 |
| chr_1 | g12102 | g12102.t28 | exon | g12102.t28.exon3 | 20939709 | 20939911 |
| chr_1 | g12102 | g12102.t28 | cds | g12102.t28.CDS3 | 20939709 | 20939772 |
| chr_1 | g12102 | g12102.t28 | exon | g12102.t28.exon4 | 20940108 | 20940413 |
| chr_1 | g12102 | g12102.t28 | TTS | g12102.t28 | 20940505 | 20940505 |
Sequences
>g12102.t28 Gene=g12102 Length=802
ATGGTCGCTAAAAAGCCAGTAAGCAAAAAGAAGGTTGTTGGTAAAAAAGTGGCTGCTGCT
CCTCTTTCAAAATCAGCAGTACAAAAGAAAACTGCTAGCAATCCATTGTTCGAAAAACGT
CCCAAGAATTATGGTATTGGTCAAAACGTTCAACCAAAACGTGATCTATCACGTTTCGTT
AGATGGCCAAAATATATTCGTATTCAGCGCCATAAAGCTATCTTGCAAAAAAGATTGAAG
GTTCCACCACCAATTAATCAATTTTCTCAAGCTTTAGATAAGCAAACAGGTGATTTTGGA
AAAATATCGTCCAGAATCAAAGTTGCAAAAAGCTGCTCGTTTGAAGAAAAAGGCTGAAGA
AAAGGTTGCAGGCAAGGATGATGCTCCATCAAAGAAGAAATTGACATTGAGAGCTGGTTG
CAACACAGTCACCAAGTTGGTTGAGCAAAAGAAGGCACAATTAGTTGTCATCTCACATGA
CGTTGATCCAATCGAATTGGTTCTCTTTTTGCCAGCCTTATGCCGTAAAATGGGAGTTCC
ATATTGCATCGTAAAGGGCAAATCACGATTGGGACGTTTGGTTCATCGCAAAACATGCAC
AACTTTAGCTTTGTGCAATGTTGATAATGCTGATCGCGCAAACTTCTCAAAGATCGTGGA
ATCAATTAAGACCAACTATAATGATCGTTATGATGAAATTCGTCGTCATTGGGGTGGTGG
TTTACTCGGACCAAAATCAATGGCTCGTATTGCTAAGGTTGAAAAGGCTAAAGCTCGTGA
ATTAGCCCAAAAACAAGGATAA
>g12102.t28 Gene=g12102 Length=118
MVAKKPVSKKKVVGKKVAAAPLSKSAVQKKTASNPLFEKRPKNYGIGQNVQPKRDLSRFV
RWPKYIRIQRHKAILQKRLKVPPPINQFSQALDKQTGDFGKISSRIKVAKSCSFEEKG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12102.t28 | Gene3D | G3DSA:3.30.1330.210 | - | 62 | 115 | 3.7E-15 |
| 6 | g12102.t28 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 50 | - |
| 1 | g12102.t28 | PANTHER | PTHR23105:SF128 | - | 12 | 102 | 8.7E-32 |
| 2 | g12102.t28 | PANTHER | PTHR23105 | RIBOSOMAL PROTEIN L7AE FAMILY MEMBER | 12 | 102 | 8.7E-32 |
| 5 | g12102.t28 | PRINTS | PR00882 | Ribosomal protein L7A family signature | 41 | 58 | 3.8E-29 |
| 3 | g12102.t28 | PRINTS | PR00882 | Ribosomal protein L7A family signature | 58 | 75 | 3.8E-29 |
| 4 | g12102.t28 | PRINTS | PR00882 | Ribosomal protein L7A family signature | 78 | 97 | 3.8E-29 |
| 7 | g12102.t28 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
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.
