General information for g11401.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 60S ribosomal protein L13a.
Parent gene
- The parent gene g11401 is located on chr_1: 15971204..15980307 (+ 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 | g11401 | g11401.t12 | isoform | g11401.t12 | 15970527 | 15971692 |
| chr_1 | g11401 | g11401.t12 | exon | g11401.t12.exon1 | 15970527 | 15970894 |
| chr_1 | g11401 | g11401.t12 | cds | g11401.t12.CDS1 | 15970859 | 15970894 |
| chr_1 | g11401 | g11401.t12 | exon | g11401.t12.exon2 | 15971117 | 15971692 |
| chr_1 | g11401 | g11401.t12 | cds | g11401.t12.CDS2 | 15971117 | 15971614 |
| chr_1 | g11401 | g11401.t12 | TTS | g11401.t12 | 15971690 | 15971690 |
| chr_1 | g11401 | g11401.t12 | TSS | g11401.t12 | NA | NA |
Sequences
>g11401.t12 Gene=g11401 Length=944
ATGTCTTACAAGTTTTCAAATAAGGTGCGTAAAAATAATTAAAATTTTTGAGTATACAAT
CAATTTGGAGTTAAATTTTTAAAACAAATCATTTTCTAAGATGATTCTCTCAATAAATTT
ACATATTATATAGTTGAGAAAGTTTTAAATTTAAAGTTCTTCAATAGATTATTGCTCGAA
AATTTTTAACCTAAAAAATAAACATGAAATTTTATTCCTTTTCTTTTTTCATTTTAGGCA
ATTGTCATTGATGGTCGTGGCCATCTCTTGGGACGATTGGCATCAATTGTCGCAAAGCAA
ATTTTAAACGGTACCAAGGTTGTTATCGTAAGATGCGAAGATTTACAACTTTCAGGTCAT
TTCTTCAGTTCTTGTCGTTCCTTCGCAAGCGCTGTAATGTCAACCCAGCTCGTGGTCCAT
TCCATTTCCGCGCACCAAGTCGTATGTTTTGGAAAGCTGTTCGCGGAATGGTTCCACATA
AAACACGCCGTGGAAAGCTTGCATTAGCTCGTTTAAAGGTCTTTGAAGGAATTCCACCAC
CATATGACAAGCAAAAGCGAGTTTGTGTTCCTCTTGCTATGAAAATTTTGTGCTTACGAT
CAGACAGAAAGTATTGCCAAGTAGGACGTGTAGCTCATGAAGTTGGTTGGCAATATAAAG
ATGTTGTAAGCAGTCTTGAAGCAAAGAGAAAGATCAAGGCACGCTTGTATTACAACCATA
AACAACGTTTGGAAAAACTTCGTCTACGTGCTACACAAAAAGTTTCAAAAGGAATCGCCA
AACAAAATTCCATTCTCAAAAAGTTCGGATATATCACATCAGAAAATGAAGTGAAGCCAG
TCGCCGCCGTCGCAGCAAAGGCATAAACTTTTGACCGAAAACATGAAATAAAGAAGTTAA
AAAGGATTCAATAAAATCAATGAACCTATTCTGAAATAATTTAA
>g11401.t12 Gene=g11401 Length=177
MRRFTTFRSFLQFLSFLRKRCNVNPARGPFHFRAPSRMFWKAVRGMVPHKTRRGKLALAR
LKVFEGIPPPYDKQKRVCVPLAMKILCLRSDRKYCQVGRVAHEVGWQYKDVVSSLEAKRK
IKARLYYNHKQRLEKLRLRATQKVSKGIAKQNSILKKFGYITSENEVKPVAAVAAKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11401.t12 | Gene3D | G3DSA:3.90.1180.10 | - | 4 | 108 | 2.7E-42 |
| 2 | g11401.t12 | PANTHER | PTHR11545:SF3 | 60S RIBOSOMAL PROTEIN L13A-RELATED | 7 | 160 | 1.6E-61 |
| 3 | g11401.t12 | PANTHER | PTHR11545 | RIBOSOMAL PROTEIN L13 | 7 | 160 | 1.6E-61 |
| 1 | g11401.t12 | Pfam | PF00572 | Ribosomal protein L13 | 18 | 69 | 8.0E-10 |
| 5 | g11401.t12 | ProSitePatterns | PS00783 | Ribosomal protein L13 signature. | 43 | 66 | - |
| 4 | g11401.t12 | SUPERFAMILY | SSF52161 | Ribosomal protein L13 | 8 | 108 | 9.03E-28 |
| 7 | g11401.t12 | TIGRFAM | TIGR01077 | L13_A_E: ribosomal protein uL13 | 8 | 108 | 2.9E-32 |
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:0015934 | large ribosomal subunit | CC |
| GO:0006412 | translation | BP |
| GO:0003735 | structural constituent of ribosome | MF |
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.
