General information for g6539.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g6539.t1 | 17548462 | 17548462 |
| chr_2 | g6539 | g6539.t1 | isoform | g6539.t1 | 17548553 | 17550536 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon1 | 17548553 | 17548927 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS1 | 17548553 | 17548927 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon2 | 17549001 | 17549205 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS2 | 17549001 | 17549205 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon3 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS3 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon4 | 17549629 | 17549992 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS4 | 17549629 | 17549992 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon5 | 17550058 | 17550212 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS5 | 17550058 | 17550212 |
| chr_2 | g6539 | g6539.t1 | exon | g6539.t1.exon6 | 17550414 | 17550536 |
| chr_2 | g6539 | g6539.t1 | cds | g6539.t1.CDS6 | 17550414 | 17550536 |
| chr_2 | g6539 | g6539.t1 | TSS | g6539.t1 | 17550902 | 17550902 |
Sequences
>g6539.t1 Gene=g6539 Length=1521
ATGGGAAACTATTATTACAAACACAATGCGTGGAAAAAAATTGTAATCAACACTGCTTTC
ATGTTAACTGGAAGTTTATTAATTTTATTTTGGCCAAACACATGGAGTTATTTATTGGCA
AAGCAGTGGCAAATTAAGCCGGGAACGCTTTTATTCAAAATATGGAGTGATCCTCCTCAG
CCAATTTATTTAGACGTTTATTTTTTTAATTGGACTAATCCACATGAATTTCAAAATCAA
TCGATAAAACCTAAATTTAATGAAGTTGGACCATACAGATTTCAAGAATATCCACAAAAA
GTCAATGTCACATACCATGATCAAAACGACACAATAAGCTACCGTAAACAAAGTCGTTTT
ATTTTTCTGCCAGATGAGAGTAAAGGACAATTAAGTGATATGATTACATCGATAAACGTA
GTTGCTTTATCATCAGCAAATCAAGCTAGAAGTTGGAATATTTTTAAAGTGAAGGGTGTT
GAACTTAGTTTATCATTTTTTGATCAGCAAATTCATCTTACAAAAACTGCTTCTGAATTG
TTGTTTGAAGGGTACGATGATCCGATAATTAACGTGGCAAAGGAGATTGCAAAAATTATG
GGTATAACAGTTCCTTTCGATCGTTTCGGTTATTTTTACTCGCGTAACGAGTCTAGTTTG
CTTACCGGTGATTTCAATGTCGATTCTGGAATTTCAACAGTTGGACAACTCAGAAAATGG
AACTATCAATCCACATCTGATCATTTTGAGGGAAGTTGTTCTAATCTCGAAGGTGCATCA
GCTGGAGAACTTTTTCCACCAGAAATAACAAACAAAATATCAACAATTTCTGTATTCTCA
CCTGAAATATGTCGAAATTTATTAATTGATTTTGAAAAAGAAATCAATGTGGATGGTATT
ACTGCAAAAAGATTTATTGGAGGTGATAGAACTGTTGATAATGGCACAAAGTATCCTGAA
AACAAGTGCTTTTTCTCGGGTGATAATGTGGCAAGTGGTGTGTTAAATGTAACAGCGTGC
CGATTGGGTGCACCAGTTTTCATGTCATTTCCACATTTTTATGCCGCTGATGAAAGCTAT
AGAAATGCAATTGAAGGTATGGCTCCAAATAAAGAGAAGCATCAATTTTATATGACCTTC
GAGCCGAAAACATCTTTACCTATCGAGATTGCAGGAAGATTTCAATTAAATGTGTTAATT
AAGCCCATTCGTAATATTAATATGTATAAAAACGTGCCCACAAAATTTTTACCGGTTGTA
TGGTTCGAGCAGCATTTTAAAGCAAGTCAAAATGTTAATCGAATTATAAAGCTATTGTTG
TGGATTCCTATTATTGGTCAAATAATTGGCTTTTTAATCGCGTTAATTGGAATTTATGGA
ATATATAAGATTTCATCTCAAAAAAGCCAAAACGAAGAAATCTCAATTATTCGTGACAAT
AATTATAATAGCATCCAAATGAACATTTCAAAAGTACCAGAGAAAAGACTGCTACCTGAA
GAAGCCTCACTTATCAATTAA
>g6539.t1 Gene=g6539 Length=506
MGNYYYKHNAWKKIVINTAFMLTGSLLILFWPNTWSYLLAKQWQIKPGTLLFKIWSDPPQ
PIYLDVYFFNWTNPHEFQNQSIKPKFNEVGPYRFQEYPQKVNVTYHDQNDTISYRKQSRF
IFLPDESKGQLSDMITSINVVALSSANQARSWNIFKVKGVELSLSFFDQQIHLTKTASEL
LFEGYDDPIINVAKEIAKIMGITVPFDRFGYFYSRNESSLLTGDFNVDSGISTVGQLRKW
NYQSTSDHFEGSCSNLEGASAGELFPPEITNKISTISVFSPEICRNLLIDFEKEINVDGI
TAKRFIGGDRTVDNGTKYPENKCFFSGDNVASGVLNVTACRLGAPVFMSFPHFYAADESY
RNAIEGMAPNKEKHQFYMTFEPKTSLPIEIAGRFQLNVLIKPIRNINMYKNVPTKFLPVV
WFEQHFKASQNVNRIIKLLLWIPIIGQIIGFLIALIGIYGIYKISSQKSQNEEISIIRDN
NYNSIQMNISKVPEKRLLPEEASLIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6539.t1 | PANTHER | PTHR11923 | SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 | 14 | 463 | 1.1E-153 |
| 3 | g6539.t1 | PANTHER | PTHR11923:SF93 | GH07959P-RELATED | 14 | 463 | 1.1E-153 |
| 8 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 57 | 78 | 9.7E-35 |
| 6 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 83 | 95 | 9.7E-35 |
| 7 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 111 | 130 | 9.7E-35 |
| 9 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 254 | 278 | 9.7E-35 |
| 4 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 329 | 353 | 9.7E-35 |
| 5 | g6539.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 376 | 397 | 9.7E-35 |
| 1 | g6539.t1 | Pfam | PF01130 | CD36 family | 19 | 461 | 5.4E-137 |
| 13 | g6539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 13 | - |
| 15 | g6539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 14 | 32 | - |
| 14 | g6539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 437 | - |
| 16 | g6539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 438 | 462 | - |
| 12 | g6539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 463 | 506 | - |
| 11 | g6539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 10 | g6539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 439 | 461 | - |
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.
