General information for g6539.t9
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.t9 | TTS | g6539.t9 | 17548462 | 17548462 |
| chr_2 | g6539 | g6539.t9 | isoform | g6539.t9 | 17549196 | 17550536 |
| chr_2 | g6539 | g6539.t9 | exon | g6539.t9.exon1 | 17549196 | 17549205 |
| chr_2 | g6539 | g6539.t9 | cds | g6539.t9.CDS1 | 17549196 | 17549205 |
| chr_2 | g6539 | g6539.t9 | exon | g6539.t9.exon2 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t9 | cds | g6539.t9.CDS2 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t9 | exon | g6539.t9.exon3 | 17549629 | 17549992 |
| chr_2 | g6539 | g6539.t9 | cds | g6539.t9.CDS3 | 17549629 | 17549871 |
| chr_2 | g6539 | g6539.t9 | exon | g6539.t9.exon4 | 17550058 | 17550209 |
| chr_2 | g6539 | g6539.t9 | exon | g6539.t9.exon5 | 17550410 | 17550536 |
| chr_2 | g6539 | g6539.t9 | TSS | g6539.t9 | 17550902 | 17550902 |
Sequences
>g6539.t9 Gene=g6539 Length=952
ATGGGAAACTATTATTACAAACACAATGCGTGGAAAAAAATTGTAATCAACACTGCTTTC
ATGTTAACTGGAAGTTTATTAATTTTATTTTGGCCAAACACATGGAGTTATTTATTGGCA
AAGGCGATGGCAAATTAAGCCGGGAACGCTTTTATTCAAAATATGGAGTGATCCTCCTCA
GCCAATTTATTTAGACGTTTATTTTTTTAATTGGACTAATCCACATGAATTTCAAAATCA
ATCGATAAAACCTAAATTTAATGAAGTTGGACCATACAGATTTCAAGAATATCCACAAAA
AGTCAATGTCACATACCATGATCAAAACGACACAATAAGCTACCGTAAACAAAGTCGTTT
TATTTTTCTGCCAGATGAGAGTAAAGGACAATTAAGTGATATGATTACATCGATAAACGT
AGTTGCTTTATCATCAGCAAATCAAGCTAGAAGTTGGAATATTTTTAAAGTGAAGGGTGT
TGAACTTAGTTTATCATTTTTTGATCAGCAAATTCATCTTACAAAAACTGCTTCTGAATT
GTTGTTTGAAGGGTACGATGATCCGATAATTAACGTGGCAAAGGAGATTGCAAAAATTAT
GGGTATAACAGTTCCTTTCGATCGTTTCGGTTATTTTTACTCGCGTAACGAGTCTAGTTT
GCTTACCGGTGATTTCAATGTCGATTCTGGAATTTCAACAGTTGGACAACTCAGAAAATG
GAACTATCAATCCACATCTGATCATTTTGAGGGAAGTTGTTCTAATCTCGAAGGTGCATC
AGCTGGAGAACTTTTTCCACCAGAAATAACAAACAAAATATCAACAATTTCTGTATTCTC
ACCTGAAATATGTCGAAATTTATTAATTGATTTTGAAAAAGAAATCAATGTGGATGGTAT
TACTGCAAAAAGATTTATTGGAGGTGATAGAACTGTTGATAATGGCACAAAG
>g6539.t9 Gene=g6539 Length=184
MITSINVVALSSANQARSWNIFKVKGVELSLSFFDQQIHLTKTASELLFEGYDDPIINVA
KEIAKIMGITVPFDRFGYFYSRNESSLLTGDFNVDSGISTVGQLRKWNYQSTSDHFEGSC
SNLEGASAGELFPPEITNKISTISVFSPEICRNLLIDFEKEINVDGITAKRFIGGDRTVD
NGTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6539.t9 | PANTHER | PTHR11923 | SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 | 2 | 184 | 0 |
| 3 | g6539.t9 | PANTHER | PTHR11923:SF93 | GH07959P-RELATED | 2 | 184 | 0 |
| 1 | g6539.t9 | Pfam | PF01130 | CD36 family | 2 | 183 | 0 |
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.
