Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein croquemort.

Parent gene

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 g13495 g13495.t5 isoform g13495.t5 30513336 30514847
chr_1 g13495 g13495.t5 exon g13495.t5.exon1 30513336 30513695
chr_1 g13495 g13495.t5 cds g13495.t5.CDS1 30513369 30513695
chr_1 g13495 g13495.t5 exon g13495.t5.exon2 30514713 30514847
chr_1 g13495 g13495.t5 cds g13495.t5.CDS2 30514713 30514847
chr_1 g13495 g13495.t5 TSS g13495.t5 NA NA
chr_1 g13495 g13495.t5 TTS g13495.t5 NA NA

Sequences

>g13495.t5 Gene=g13495 Length=495
ATGAGCGCATCGAATTTAAATAAAAATACGCGTGTTATTTATCTAATTGTGATAGTTTTA
GGAGTTACAACAAATTTAGCTGGAATTTTACTTATAAATTATTTTCCTGAAATTTTCGAC
AGTTTGTTCTTCAAAAAACTTGCTCTGCAACCAGGATCAAAAAGTTATGAATTTTGGAGT
GAACCTCCACAGCCACTTTATCTGGATGTTTATCTTTTTAACTGGACAAATCCAGAAGAT
TTTACAAATAAATCAGTAAATCCACGTTTCGATGAAATTGGCCCATTTCGATTTCAAGAG
TTTCCAAGTAAGGTCAATGTAAAGTTTCATAATGATAACGGAACTGTGAGCTATCGAAAA
TCGAGTAAATACATTTTTGTGCCAGAAGAGAGCGGCGGTCGTATGGATGATGTCATCACT
TCAATCAATGTCATAGCTCTCGTAAGTGGTAATAAAACTTGATTAATATCACTTAATTCA
ATTTTTCATAACAGG

>g13495.t5 Gene=g13495 Length=153
MSASNLNKNTRVIYLIVIVLGVTTNLAGILLINYFPEIFDSLFFKKLALQPGSKSYEFWS
EPPQPLYLDVYLFNWTNPEDFTNKSVNPRFDEIGPFRFQEFPSKVNVKFHNDNGTVSYRK
SSKYIFVPEESGGRMDDVITSINVIALVSGNKT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g13495.t5 PANTHER PTHR11923 SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 11 150 2.9E-44
3 g13495.t5 PANTHER PTHR11923:SF93 GH07959P-RELATED 11 150 2.9E-44
5 g13495.t5 PRINTS PR01609 Adhesion molecule CD36 family signature 61 82 3.1E-15
4 g13495.t5 PRINTS PR01609 Adhesion molecule CD36 family signature 87 99 3.1E-15
6 g13495.t5 PRINTS PR01609 Adhesion molecule CD36 family signature 115 134 3.1E-15
1 g13495.t5 Pfam PF01130 CD36 family 19 147 2.2E-42
8 g13495.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
10 g13495.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
9 g13495.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 153 -
7 g13495.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -

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