Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative CD9 antigen.

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_3 g2706 g2706.t1 TTS g2706.t1 19780113 19780113
chr_3 g2706 g2706.t1 isoform g2706.t1 19780285 19793146
chr_3 g2706 g2706.t1 exon g2706.t1.exon1 19780285 19780443
chr_3 g2706 g2706.t1 cds g2706.t1.CDS1 19780285 19780443
chr_3 g2706 g2706.t1 exon g2706.t1.exon2 19780515 19780603
chr_3 g2706 g2706.t1 cds g2706.t1.CDS2 19780515 19780603
chr_3 g2706 g2706.t1 exon g2706.t1.exon3 19780665 19780962
chr_3 g2706 g2706.t1 cds g2706.t1.CDS3 19780665 19780962
chr_3 g2706 g2706.t1 exon g2706.t1.exon4 19781031 19781225
chr_3 g2706 g2706.t1 cds g2706.t1.CDS4 19781031 19781225
chr_3 g2706 g2706.t1 exon g2706.t1.exon5 19793087 19793146
chr_3 g2706 g2706.t1 cds g2706.t1.CDS5 19793087 19793146
chr_3 g2706 g2706.t1 TSS g2706.t1 19793361 19793361

Sequences

>g2706.t1 Gene=g2706 Length=801
ATGAATTGCTGCTGTTCTATCGTTAAATTTTTCGTCATATTGATGAATCTTGTATTCTGG
ATTGCTGGCATCGGAATAGTTGCATTAGCAGTTTGGATGTTGATCGATCCAACATTTATG
ATCTCGCTTACTCAAGAACACCAAAATTATCAATATGCACTTTTCATTCTGTTAGGCATT
GGTATTCTACTTGTTCTGCTCGCCTTCTGTGGATGTTGTGGAGCACTTAAGGAATCACAA
TGCATGCTTGTTTCGTTCTTTTGCTGTATGCTCATTGTGCTTACTGCGGAAATTGCTGCA
GGGGTATGGAGTTATCAAAATTCTGATAAACTTGAATCATTCGTTAAAGCTAACTTCCAA
TACACAATTAACAACGAATATAAAGTGATTGAAGCGAGAACTGAAATTGTGGATGTCATT
CAAACTCATTTGCAATGCTGTGGTGTGAACGGACCATCAGATTGGAGTAATTCAAAATAT
AACGGTGCCAAGAGCGGCAATATTGTTGACTATGCAATCACTTCAAAACTCGCATACGCT
GTTCCACCATCATGTTGTAAGAATGGAACTGAGAAATCATTATGTGAAACATCAAGAAAA
GGCACGATAACAACAAGTCTTAATCCAGTAATCTATAATAAAGGCTGCATGGAAAAAGTC
GTGGCAGAAGTAAAACGAAACTTGCATTATGTTCTATTGGGCGGATTAATAATTATTGCT
GTGCAGCTATTTGGGATATTACTAGTGTTGTGTTTATGCTGTGCCGTCAAACGTAACAAA
GACGATGACTACAAAGATTAA

>g2706.t1 Gene=g2706 Length=266
MNCCCSIVKFFVILMNLVFWIAGIGIVALAVWMLIDPTFMISLTQEHQNYQYALFILLGI
GILLVLLAFCGCCGALKESQCMLVSFFCCMLIVLTAEIAAGVWSYQNSDKLESFVKANFQ
YTINNEYKVIEARTEIVDVIQTHLQCCGVNGPSDWSNSKYNGAKSGNIVDYAITSKLAYA
VPPSCCKNGTEKSLCETSRKGTITTSLNPVIYNKGCMEKVVAEVKRNLHYVLLGGLIIIA
VQLFGILLVLCLCCAVKRNKDDDYKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2706.t1 Gene3D G3DSA:1.10.1450.10 Tetraspanin 105 226 2.8E-10
2 g2706.t1 PANTHER PTHR19282:SF460 TETRASPANIN 1 259 1.3E-65
3 g2706.t1 PANTHER PTHR19282 TETRASPANIN 1 259 1.3E-65
19 g2706.t1 PIRSF PIRSF002419 Tetraspanin 1 266 3.2E-61
5 g2706.t1 PRINTS PR00259 Transmembrane four family signature 10 33 7.0E-37
4 g2706.t1 PRINTS PR00259 Transmembrane four family signature 50 76 7.0E-37
6 g2706.t1 PRINTS PR00259 Transmembrane four family signature 77 105 7.0E-37
7 g2706.t1 PRINTS PR00259 Transmembrane four family signature 230 256 7.0E-37
1 g2706.t1 Pfam PF00335 Tetraspanin family 8 255 1.1E-53
11 g2706.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g2706.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
13 g2706.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
16 g2706.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 76 -
12 g2706.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 82 -
18 g2706.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 83 105 -
14 g2706.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 229 -
15 g2706.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 230 256 -
10 g2706.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 257 266 -
8 g2706.t1 SUPERFAMILY SSF48652 Tetraspanin 105 226 4.05E-13
22 g2706.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
20 g2706.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
21 g2706.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 83 105 -
23 g2706.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 230 252 -

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:0016021 integral component of membrane CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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.

Raw TPM values