General information for g13169.t54
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g13169 is located on chr_1: 28316986..28327569 (+ 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 | g13169 | g13169.t54 | TSS | g13169.t54 | 28316629 | 28316629 |
| chr_1 | g13169 | g13169.t54 | isoform | g13169.t54 | 28316740 | 28317659 |
| chr_1 | g13169 | g13169.t54 | exon | g13169.t54.exon1 | 28316740 | 28317310 |
| chr_1 | g13169 | g13169.t54 | cds | g13169.t54.CDS1 | 28317095 | 28317310 |
| chr_1 | g13169 | g13169.t54 | exon | g13169.t54.exon2 | 28317377 | 28317659 |
| chr_1 | g13169 | g13169.t54 | cds | g13169.t54.CDS2 | 28317377 | 28317634 |
| chr_1 | g13169 | g13169.t54 | TTS | g13169.t54 | 28317861 | 28317861 |
Sequences
>g13169.t54 Gene=g13169 Length=854
ATGTCTCTTACTTGGACTTTAATCGGTGCGTAAAAGTTTTTCTCGAAAATAAATTTATTT
TGAAAACATTCCCGTACATTCTAAAATTTACAGCTGGATTTTTGTATGCTGAAGTTGCTG
TTGTTCTTTTATTAGTATTGCCTGGTAAGGAAATTTTTGATATTACAAATATTGTGAAAT
TTTTTTGGAAATGTAGCAATTCTATTTTTAAACTGCTTATTTAGTCTTTAGTGCATCCAA
ATGGAATCGTTTCTTCAAATCAAGATTTCTGTCAGCTCTCTCTCGGCAAGCACAGATTTA
CTTTTATTTGATGCTTGGTGTTTTGGTAATCTTTTTGCTTGAGGCTATTAGAGAAATGCG
TAAATACAGCAGCAGTGAAGAGGAAACTACTCTTAATTTGGGAATGCAACATTCAATGAG
ACTCTTCCGTGCTCAACGCAACTTTTACATCTCTGGGTTTGCCATTTTCTTGTCATTGGT
CATTAGACGATTGATTATTTTAATCACAACACAAGCATCGTTAATTGCAAATTCTGAAGC
AAGCATGAAACAAGCACAGTCCGCAACACAGGCTGCTCGTCATTTAATGGCCGAAAAGAA
AACTGATGGTGGTTCTGCTAACACTGCTAATAGTGATAATAAAGCTGATGATGATAAGGA
AAAATTACAAAACAAGATTAAAGAATTGGAAGCTGAATTGAAAAAGGAACGAAAGGATAA
AGAAGCATTAAAATCGCAAGCTGATTCACTCAACAGAGAATATGATCGATTGACAGAAGA
GTACAGCAAATTGCAGAACAAGCAGGCTGCTGGTGACAAGTCAGACTAAGCTATTCGAAT
ATTTGTGCATCACG
>g13169.t54 Gene=g13169 Length=157
MRKYSSSEEETTLNLGMQHSMRLFRAQRNFYISGFAIFLSLVIRRLIILITTQASLIANS
EASMKQAQSATQAARHLMAEKKTDGGSANTANSDNKADDDKEKLQNKIKELEAELKKERK
DKEALKSQADSLNREYDRLTEEYSKLQNKQAAGDKSD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g13169.t54 | Coils | Coil | Coil | 94 | 149 | - |
| 7 | g13169.t54 | Gene3D | G3DSA:1.20.5.110 | - | 87 | 146 | 7.3E-6 |
| 6 | g13169.t54 | MobiDBLite | mobidb-lite | consensus disorder prediction | 61 | 105 | - |
| 3 | g13169.t54 | PANTHER | PTHR12701:SF50 | LP10861P | 1 | 151 | 1.8E-38 |
| 4 | g13169.t54 | PANTHER | PTHR12701 | BCR-ASSOCIATED PROTEIN, BAP | 1 | 151 | 1.8E-38 |
| 2 | g13169.t54 | Pfam | PF05529 | Bap31/Bap29 transmembrane region | 6 | 62 | 5.9E-17 |
| 1 | g13169.t54 | Pfam | PF18035 | Bap31/Bap29 cytoplasmic coiled-coil domain | 106 | 157 | 4.8E-18 |
| 9 | g13169.t54 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 29 | - |
| 11 | g13169.t54 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 50 | - |
| 10 | g13169.t54 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 51 | 157 | - |
| 5 | g13169.t54 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 48 | - |
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:0006886 | intracellular protein transport | BP |
| GO:0005783 | endoplasmic reticulum | CC |
| GO:0016021 | integral component of membrane | CC |
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.
