General information for g6539.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein peste.
Parent gene
- The parent gene g6539 is located on chr_2: 17550070..17550905 (- 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 | g6539 | g6539.t4 | TTS | g6539.t4 | 17548174 | 17548174 |
| chr_2 | g6539 | g6539.t4 | isoform | g6539.t4 | 17548181 | 17550536 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon1 | 17548181 | 17548927 |
| chr_2 | g6539 | g6539.t4 | cds | g6539.t4.CDS1 | 17548553 | 17548927 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon2 | 17549001 | 17549205 |
| chr_2 | g6539 | g6539.t4 | cds | g6539.t4.CDS2 | 17549001 | 17549105 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon3 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon4 | 17549625 | 17549992 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon5 | 17550058 | 17550212 |
| chr_2 | g6539 | g6539.t4 | exon | g6539.t4.exon6 | 17550410 | 17550536 |
| chr_2 | g6539 | g6539.t4 | TSS | g6539.t4 | 17550902 | 17550902 |
Sequences
>g6539.t4 Gene=g6539 Length=1901
ATGGGAAACTATTATTACAAACACAATGCGTGGAAAAAAATTGTAATCAACACTGCTTTC
ATGTTAACTGGAAGTTTATTAATTTTATTTTGGCCAAACACATGGAGTTATTTATTGGCA
AAGGCGACAGTGGCAAATTAAGCCGGGAACGCTTTTATTCAAAATATGGAGTGATCCTCC
TCAGCCAATTTATTTAGACGTTTATTTTTTTAATTGGACTAATCCACATGAATTTCAAAA
TCAATCGATAAAACCTAAATTTAATGAAGTTGGACCATACAGATTTCAAGAATATCCACA
AAAAGTCAATGTCACATACCATGATCAAAACGACACAATAAGCTACCGTAAACAAAGTCG
TTTTATTTTTCTGCCAGATGAGAGTAAAGGACAATTAAGTGATATGATTACATCGATAAA
CGTAGTTGCTTTATCATCAGCAAATCAAGCTAGAAGTTGGAATATTTTTAAAGTGAAGGG
TGTTGAACTTAGTTTATCATTTTTTGATCAGCAAATTCATCTTACAAAAACTGCTTCTGA
ATTGTTGTTTGAAGGGTACGATGATCCGATAATTAACGTGGCAAAGGAGATTGCAAAAAT
TATGGGTATAACAGTTCCTTTCGATCGTTTCGGTTATTTTTACTCGGTGACGTAACGAGT
CTAGTTTGCTTACCGGTGATTTCAATGTCGATTCTGGAATTTCAACAGTTGGACAACTCA
GAAAATGGAACTATCAATCCACATCTGATCATTTTGAGGGAAGTTGTTCTAATCTCGAAG
GTGCATCAGCTGGAGAACTTTTTCCACCAGAAATAACAAACAAAATATCAACAATTTCTG
TATTCTCACCTGAAATATGTCGAAATTTATTAATTGATTTTGAAAAAGAAATCAATGTGG
ATGGTATTACTGCAAAAAGATTTATTGGAGGTGATAGAACTGTTGATAATGGCACAAAGT
ATCCTGAAAACAAGTGCTTTTTCTCGGGTGATAATGTGGCAAGTGGTGTGTTAAATGTAA
CAGCGTGCCGATTGGGTGCACCAGTTTTCATGTCATTTCCACATTTTTATGCCGCTGATG
AAAGCTATAGAAATGCAATTGAAGGTATGGCTCCAAATAAAGAGAAGCATCAATTTTATA
TGACCTTCGAGCCGAAAACATCTTTACCTATCGAGATTGCAGGAAGATTTCAATTAAATG
TGTTAATTAAGCCCATTCGTAATATTAATATGTATAAAAACGTGCCCACAAAATTTTTAC
CGGTTGTATGGTTCGAGCAGCATTTTAAAGCAAGTCAAAATGTTAATCGAATTATAAAGC
TATTGTTGTGGATTCCTATTATTGGTCAAATAATTGGCTTTTTAATCGCGTTAATTGGAA
TTTATGGAATATATAAGATTTCATCTCAAAAAAGCCAAAACGAAGAAATCTCAATTATTC
GTGACAATAATTATAATAGCATCCAAATGAACATTTCAAAAGTACCAGAGAAAAGACTGC
TACCTGAAGAAGCCTCACTTATCAATTAATATTAATTTATTGTACCCTATTTATAAGATT
TCTTCAATGAAGTATGTTATAGTATTTAAATGCACTCTCAAATAATAAATTTTATAAACG
AACTTAAGAAGTTATCATTAAATACGTTTATAGGATAAACGATGGTTTATTAATTTGTTT
TGTATGCTTTAAGCATAATCGTTACATAAAATTAAGAGACAATAAGTGACTAATAAAAAA
TGTGTGCATACTGACAAAATAAAATAAATTTTGAACAAAGTCATTGAGTTGATAACAGAA
TAAATTATCACACAAAACATGGATTGTTATTGTAAATAATGCTCTGCATTTTGGTATTTA
AAATTTGTGTTTCAAGTGAATAAAAGTTATGAAAAAATTTT
>g6539.t4 Gene=g6539 Length=159
MSFPHFYAADESYRNAIEGMAPNKEKHQFYMTFEPKTSLPIEIAGRFQLNVLIKPIRNIN
MYKNVPTKFLPVVWFEQHFKASQNVNRIIKLLLWIPIIGQIIGFLIALIGIYGIYKISSQ
KSQNEEISIIRDNNYNSIQMNISKVPEKRLLPEEASLIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6539.t4 | PANTHER | PTHR11923 | SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 | 1 | 117 | 1.0E-34 |
| 3 | g6539.t4 | PANTHER | PTHR11923:SF93 | GH07959P-RELATED | 1 | 117 | 1.0E-34 |
| 1 | g6539.t4 | Pfam | PF01130 | CD36 family | 1 | 114 | 4.9E-35 |
| 5 | g6539.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 90 | - |
| 7 | g6539.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 91 | 115 | - |
| 6 | g6539.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 116 | 159 | - |
| 4 | g6539.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 92 | 114 | - |
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:0016020 | 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.
