General information for g11187.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g11187 is located on chr_1: 14481402..14482827 (- 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 | g11187 | g11187.t4 | isoform | g11187.t4 | 14479718 | 14482016 |
| chr_1 | g11187 | g11187.t4 | exon | g11187.t4.exon1 | 14479718 | 14479946 |
| chr_1 | g11187 | g11187.t4 | cds | g11187.t4.CDS1 | 14479718 | 14479946 |
| chr_1 | g11187 | g11187.t4 | exon | g11187.t4.exon2 | 14480016 | 14480619 |
| chr_1 | g11187 | g11187.t4 | cds | g11187.t4.CDS2 | 14480016 | 14480619 |
| chr_1 | g11187 | g11187.t4 | exon | g11187.t4.exon3 | 14481818 | 14481887 |
| chr_1 | g11187 | g11187.t4 | cds | g11187.t4.CDS3 | 14481818 | 14481887 |
| chr_1 | g11187 | g11187.t4 | exon | g11187.t4.exon4 | 14481951 | 14482016 |
| chr_1 | g11187 | g11187.t4 | cds | g11187.t4.CDS4 | 14481951 | 14482016 |
| chr_1 | g11187 | g11187.t4 | TSS | g11187.t4 | 14482053 | 14482053 |
| chr_1 | g11187 | g11187.t4 | TTS | g11187.t4 | NA | NA |
Sequences
>g11187.t4 Gene=g11187 Length=969
ATGTTAAGCACGAGATTTTTAAAAGATCCATTTAAGGAAATTGTGAGAAAGTTCAGTAAT
TCAACTAATAAACAAGTGAAAAAAGTATTTTCGGGAATACAGCCAACTGGAAATTTACAT
TTAGGCAATTATTTCGGGTGGGGTTTGAAAGCACTTTCTGTATTAATAACGGTGAAAATC
AAGATTATTTTGCTGTTCCTTTTCTTGGGAGGTGGAATTTTTTATGGTCTAAAAGTATGG
CAAGGAACTGCACTTGGATGTCCTGAACCAATTATTCAAGAAGTGAAACATCATGATGGA
ATTATTCCCTATCATTCACACTTTTCTGATATTTCGTATTCTGCACCACCACCAGATGCA
TTTGGCGGTTATAATGGTTTTAGTGGATATAGTGGTGCTGATATAGGCGGAATTTATTCA
AATACACCTGCCTCACCGTCTTTTAATGGTCCAACAGGTTTTAGTAATGGAGCAGCAGCA
ACAGGAAGTGGAGCATCTGTGGGAACAATTGACGCAGGATCAGTTGTAGGTCCATCAAAT
ACTTATTTACCACCAAGTAGCCGAAGAAGAAGAGTAAGCGGAAATGCTAGAAGTGATAGC
TCAAGCGAATCTATTTCATCCATGTTCACTGATCTCATGTTTCGTTTTCTTGGAGTGAAC
ACTGATTCATGCAAGAGACGATTCGTTTGTGAGTTAGAATTTAGAAATCCATTCGTTGGC
TATGCTATGAATTACATTGGTGAATTTAGAATGGAAAAAAATAGTCCAGAATCACCTAAG
AAATTTTCTGATTGCGCTAAATTATATGCCGATTGTGAAGTTCCAAAAGAACATACATTC
GCCACAAAGAAACGTAGACGTTATTATTTGAAGAAGAGATTGAATCAAACAACGGTTGAA
GAAAAAGAAGAAACTACAATCAACCCAAACAATGATTTAGTTACAAAATACGTTAAGAAT
CAAGAGTAA
>g11187.t4 Gene=g11187 Length=322
MLSTRFLKDPFKEIVRKFSNSTNKQVKKVFSGIQPTGNLHLGNYFGWGLKALSVLITVKI
KIILLFLFLGGGIFYGLKVWQGTALGCPEPIIQEVKHHDGIIPYHSHFSDISYSAPPPDA
FGGYNGFSGYSGADIGGIYSNTPASPSFNGPTGFSNGAAATGSGASVGTIDAGSVVGPSN
TYLPPSSRRRRVSGNARSDSSSESISSMFTDLMFRFLGVNTDSCKRRFVCELEFRNPFVG
YAMNYIGEFRMEKNSPESPKKFSDCAKLYADCEVPKEHTFATKKRRRYYLKKRLNQTTVE
EKEETTINPNNDLVTKYVKNQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11187.t4 | Gene3D | G3DSA:3.40.50.620 | HUPs | 17 | 67 | 6.2E-7 |
| 4 | g11187.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 178 | 200 | - |
| 7 | g11187.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 50 | - |
| 8 | g11187.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 51 | 75 | - |
| 6 | g11187.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 76 | 322 | - |
| 3 | g11187.t4 | ProSitePatterns | PS00178 | Aminoacyl-transfer RNA synthetases class-I signature. | 35 | 44 | - |
| 2 | g11187.t4 | SUPERFAMILY | SSF52374 | Nucleotidylyl transferase | 21 | 47 | 7.15E-5 |
| 1 | g11187.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 52 | 74 | - |
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:0005524 | ATP binding | MF |
| GO:0006418 | tRNA aminoacylation for protein translation | BP |
| GO:0000166 | nucleotide binding | MF |
| GO:0004812 | aminoacyl-tRNA ligase activity | 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.
