Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative CD63 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_2 g4424 g4424.t1 TTS g4424.t1 2114178 2114178
chr_2 g4424 g4424.t1 isoform g4424.t1 2114250 2115133
chr_2 g4424 g4424.t1 exon g4424.t1.exon1 2114250 2114498
chr_2 g4424 g4424.t1 cds g4424.t1.CDS1 2114250 2114498
chr_2 g4424 g4424.t1 exon g4424.t1.exon2 2114555 2114767
chr_2 g4424 g4424.t1 cds g4424.t1.CDS2 2114555 2114767
chr_2 g4424 g4424.t1 exon g4424.t1.exon3 2114829 2115017
chr_2 g4424 g4424.t1 cds g4424.t1.CDS3 2114829 2115017
chr_2 g4424 g4424.t1 exon g4424.t1.exon4 2115071 2115133
chr_2 g4424 g4424.t1 cds g4424.t1.CDS4 2115071 2115133
chr_2 g4424 g4424.t1 TSS g4424.t1 2115424 2115424

Sequences

>g4424.t1 Gene=g4424 Length=714
ATGTCTAACACAAGTGAGGCATGCATCAAATATACTTTGTTCATTTTCAACTTTATATTT
GTGATCACTGGGATCATAATTTTGAGTGTAGGCTTGTCAGTCCAAGGAGTCTACCATGGA
TATAGTGAATTTTTGAGCAGTCAATTTTTGACCTTGCCCGTATTTCTTGTCGTTATTGGA
AGCATAATTTTCTTTGTTGCATTCTTTGGCTGCTATGGAGCTATGCGTGAAAATTACTGC
ATGATATTGACTTTTTGTGGATTATTAACAATAATATTTATTCTCGAATTGGCGGCTGGC
ATTACTGGATATATTTTGAAAAATTCTACAAGTTCACTCATTTCAGCTACTCTTGAACCT
ACTATGCATGACTATACGAATCCTGATAAAAAACATATAACTTATGCATGGGATGATATT
CAAAGTAAATTTTCTTGCTGTGGACTTGAAAGCTTTGAAGATTGGCAAAAAGCTGTTAAT
GGCACACCATTAAGTTGCTGTGAGATTCCTCATGGTATCTTGGATAAATTCACATGTGAG
AATGGCACAGAAACATTGCATAGTGAAGGATGCGTGAAATCTTTTGGTAATTTCATTCAG
TCACATGCAAAGTCATTGGGTGTTGCGGGAATAGTCTTAGCTATAGTGCAGCTATTTGGT
TTATTATTTGCATGTATAATTACAAGAACTATTAAAAAACATCGTGGGTATTAA

>g4424.t1 Gene=g4424 Length=237
MSNTSEACIKYTLFIFNFIFVITGIIILSVGLSVQGVYHGYSEFLSSQFLTLPVFLVVIG
SIIFFVAFFGCYGAMRENYCMILTFCGLLTIIFILELAAGITGYILKNSTSSLISATLEP
TMHDYTNPDKKHITYAWDDIQSKFSCCGLESFEDWQKAVNGTPLSCCEIPHGILDKFTCE
NGTETLHSEGCVKSFGNFIQSHAKSLGVAGIVLAIVQLFGLLFACIITRTIKKHRGY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4424.t1 CDD cd03127 tetraspanin_LEL 104 203 1.66829E-17
9 g4424.t1 Gene3D G3DSA:1.10.1450.10 Tetraspanin 106 202 5.2E-12
2 g4424.t1 PANTHER PTHR19282 TETRASPANIN 4 227 3.5E-48
3 g4424.t1 PANTHER PTHR19282:SF456 TETRASPANIN 4 227 3.5E-48
19 g4424.t1 PIRSF PIRSF002419 Tetraspanin 1 237 7.8E-55
7 g4424.t1 PRINTS PR00259 Transmembrane four family signature 11 34 1.2E-38
4 g4424.t1 PRINTS PR00259 Transmembrane four family signature 49 75 1.2E-38
5 g4424.t1 PRINTS PR00259 Transmembrane four family signature 76 104 1.2E-38
6 g4424.t1 PRINTS PR00259 Transmembrane four family signature 205 231 1.2E-38
1 g4424.t1 Pfam PF00335 Tetraspanin family 9 228 4.2E-53
10 g4424.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
16 g4424.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
14 g4424.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 53 -
18 g4424.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 75 -
12 g4424.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 81 -
15 g4424.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 82 106 -
13 g4424.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 107 205 -
17 g4424.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 206 227 -
11 g4424.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 228 237 -
25 g4424.t1 ProSitePatterns PS00421 Transmembrane 4 family signature. 60 82 -
8 g4424.t1 SUPERFAMILY SSF48652 Tetraspanin 104 202 4.32E-14
24 g4424.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
23 g4424.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
21 g4424.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 101 -
22 g4424.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 205 227 -

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. There were no conditions that were differentially expressed