General information for g6539.t7
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.t7 | TTS | g6539.t7 | 17548462 | 17548462 |
| chr_2 | g6539 | g6539.t7 | isoform | g6539.t7 | 17548553 | 17550905 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon1 | 17548553 | 17548927 |
| chr_2 | g6539 | g6539.t7 | cds | g6539.t7.CDS1 | 17548553 | 17548927 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon2 | 17549001 | 17549205 |
| chr_2 | g6539 | g6539.t7 | cds | g6539.t7.CDS2 | 17549001 | 17549205 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon3 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t7 | cds | g6539.t7.CDS3 | 17549266 | 17549564 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon4 | 17549629 | 17549992 |
| chr_2 | g6539 | g6539.t7 | cds | g6539.t7.CDS4 | 17549629 | 17549871 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon5 | 17550058 | 17550212 |
| chr_2 | g6539 | g6539.t7 | exon | g6539.t7.exon6 | 17550410 | 17550905 |
| chr_2 | g6539 | g6539.t7 | TSS | g6539.t7 | 17550902 | 17550902 |
Sequences
>g6539.t7 Gene=g6539 Length=1894
ATTTAAGTTTGTTTCGCGCATAAGAGAACATCAAAATATTTTATTCTCTCACTCTCACGT
GTCTTTCTGTTCGTATTACAAAATTTTTGTTATCATTTTACTTTTGTTTTGTTCATGATC
AAGTGACACTCACATAATATAAGCAATTAAATTTATAAATCTAAAATATTGCATGCAGTG
ATATCATGTGTTATTATAAAAATGTGAATAAATATTTTATGTGAAATATTGTTTTGAAAG
AATAATACGAAATTGATTTTTTATAATTCTATTTATAAAAAGTGTACAAAAGAGAGGAAA
ATAACTACATAGATAGTTAGTGATTTCATATAAAAACGAAATAAAAAAGATTCAAGTGCA
GTTTTAATTATGGGAAACTATTATTACAAACACAATGCGTGGAAAAAAATTGTAATCAAC
ACTGCTTTCATGTTAACTGGAAGTTTATTAATTTTATTTTGGCCAAACACATGGAGTTAT
TTATTGGCAAAGGCGACAGTGGCAAATTAAGCCGGGAACGCTTTTATTCAAAATATGGAG
TGATCCTCCTCAGCCAATTTATTTAGACGTTTATTTTTTTAATTGGACTAATCCACATGA
ATTTCAAAATCAATCGATAAAACCTAAATTTAATGAAGTTGGACCATACAGATTTCAAGA
ATATCCACAAAAAGTCAATGTCACATACCATGATCAAAACGACACAATAAGCTACCGTAA
ACAAAGTCGTTTTATTTTTCTGCCAGATGAGAGTAAAGGACAATTAAGTGATATGATTAC
ATCGATAAACGTAGTTGCTTTATCATCAGCAAATCAAGCTAGAAGTTGGAATATTTTTAA
AGTGAAGGGTGTTGAACTTAGTTTATCATTTTTTGATCAGCAAATTCATCTTACAAAAAC
TGCTTCTGAATTGTTGTTTGAAGGGTACGATGATCCGATAATTAACGTGGCAAAGGAGAT
TGCAAAAATTATGGGTATAACAGTTCCTTTCGATCGTTTCGGTTATTTTTACTCGCGTAA
CGAGTCTAGTTTGCTTACCGGTGATTTCAATGTCGATTCTGGAATTTCAACAGTTGGACA
ACTCAGAAAATGGAACTATCAATCCACATCTGATCATTTTGAGGGAAGTTGTTCTAATCT
CGAAGGTGCATCAGCTGGAGAACTTTTTCCACCAGAAATAACAAACAAAATATCAACAAT
TTCTGTATTCTCACCTGAAATATGTCGAAATTTATTAATTGATTTTGAAAAAGAAATCAA
TGTGGATGGTATTACTGCAAAAAGATTTATTGGAGGTGATAGAACTGTTGATAATGGCAC
AAAGTATCCTGAAAACAAGTGCTTTTTCTCGGGTGATAATGTGGCAAGTGGTGTGTTAAA
TGTAACAGCGTGCCGATTGGGTGCACCAGTTTTCATGTCATTTCCACATTTTTATGCCGC
TGATGAAAGCTATAGAAATGCAATTGAAGGTATGGCTCCAAATAAAGAGAAGCATCAATT
TTATATGACCTTCGAGCCGAAAACATCTTTACCTATCGAGATTGCAGGAAGATTTCAATT
AAATGTGTTAATTAAGCCCATTCGTAATATTAATATGTATAAAAACGTGCCCACAAAATT
TTTACCGGTTGTATGGTTCGAGCAGCATTTTAAAGCAAGTCAAAATGTTAATCGAATTAT
AAAGCTATTGTTGTGGATTCCTATTATTGGTCAAATAATTGGCTTTTTAATCGCGTTAAT
TGGAATTTATGGAATATATAAGATTTCATCTCAAAAAAGCCAAAACGAAGAAATCTCAAT
TATTCGTGACAATAATTATAATAGCATCCAAATGAACATTTCAAAAGTACCAGAGAAAAG
ACTGCTACCTGAAGAAGCCTCACTTATCAATTAA
>g6539.t7 Gene=g6539 Length=373
MITSINVVALSSANQARSWNIFKVKGVELSLSFFDQQIHLTKTASELLFEGYDDPIINVA
KEIAKIMGITVPFDRFGYFYSRNESSLLTGDFNVDSGISTVGQLRKWNYQSTSDHFEGSC
SNLEGASAGELFPPEITNKISTISVFSPEICRNLLIDFEKEINVDGITAKRFIGGDRTVD
NGTKYPENKCFFSGDNVASGVLNVTACRLGAPVFMSFPHFYAADESYRNAIEGMAPNKEK
HQFYMTFEPKTSLPIEIAGRFQLNVLIKPIRNINMYKNVPTKFLPVVWFEQHFKASQNVN
RIIKLLLWIPIIGQIIGFLIALIGIYGIYKISSQKSQNEEISIIRDNNYNSIQMNISKVP
EKRLLPEEASLIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6539.t7 | PANTHER | PTHR11923 | SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 | 2 | 331 | 1.4E-108 |
| 3 | g6539.t7 | PANTHER | PTHR11923:SF93 | GH07959P-RELATED | 2 | 331 | 1.4E-108 |
| 6 | g6539.t7 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 121 | 145 | 1.2E-14 |
| 5 | g6539.t7 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 196 | 220 | 1.2E-14 |
| 4 | g6539.t7 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 243 | 264 | 1.2E-14 |
| 1 | g6539.t7 | Pfam | PF01130 | CD36 family | 2 | 328 | 1.6E-92 |
| 9 | g6539.t7 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 304 | - |
| 10 | g6539.t7 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 329 | - |
| 8 | g6539.t7 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 330 | 373 | - |
| 7 | g6539.t7 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 306 | 328 | - |
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. There were no conditions that were differentially expressed