Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g8185 g8185.t1 TTS g8185.t1 28961757 28961757
chr_2 g8185 g8185.t1 isoform g8185.t1 28962204 28963602
chr_2 g8185 g8185.t1 exon g8185.t1.exon1 28962204 28962247
chr_2 g8185 g8185.t1 cds g8185.t1.CDS1 28962204 28962247
chr_2 g8185 g8185.t1 exon g8185.t1.exon2 28962309 28962702
chr_2 g8185 g8185.t1 cds g8185.t1.CDS2 28962309 28962702
chr_2 g8185 g8185.t1 exon g8185.t1.exon3 28962761 28962952
chr_2 g8185 g8185.t1 cds g8185.t1.CDS3 28962761 28962952
chr_2 g8185 g8185.t1 exon g8185.t1.exon4 28963537 28963602
chr_2 g8185 g8185.t1 cds g8185.t1.CDS4 28963537 28963602
chr_2 g8185 g8185.t1 TSS g8185.t1 28963786 28963786

Sequences

>g8185.t1 Gene=g8185 Length=696
ATGGGTTTAACTTGTGGAGCATCTGTGGTCAAATATGGCATTTTTATTTTCAACCTTCTT
TGTGCTGTTGCTGGTATAGCATTGATCGTTGTTGGTGCAATTCCACTATTCAAACTTGAT
GACATTCGAGATGCCTTTCCTGAAAACAATCCAGCCACTGTTCCCATCATAATCGTCGTT
CTTGGCTCGATAATCTTTATCATCAGTTTCTTTGGATGTTGTGGAGCTATTAGAGAAAAT
CAGTGTATGGTTTCAACGTACGCATTTTTCCTACTCATATTGGTCGTTCTTCAAATTGTT
ATCGCCGTTTTCGCATTTATGTATACAGGTGAACTTGCGAAAGCTGCAGAAAATGGTTTC
AATAAATTATGGGAAAACAGAGACACAAATAATGAAACAAGAATTGCTATCGAAGGCATA
CAACGCGGACTTCGCTGTTGTGGTTCAGCTGGACCCGCTGATTGGGGATTATTAAATATT
CCATCTTCATGCTGTGATGATGGAGTTATAGCATGCACAGTGTCGAACGCTCATTCAGAT
GGATGTGCTACACTTCTTTCCAACTTTGTCAATGATAGTGGACTCTTGATTGCATGGTTT
GCAATTGTCTTTGCTGGTATTGAACTTGTTGGTGTAATCTTCGCCTGTTGTCTGGCCAAT
TCAATTCGAAATGCAAACAGAAGACAATATGCATAA

>g8185.t1 Gene=g8185 Length=231
MGLTCGASVVKYGIFIFNLLCAVAGIALIVVGAIPLFKLDDIRDAFPENNPATVPIIIVV
LGSIIFIISFFGCCGAIRENQCMVSTYAFFLLILVVLQIVIAVFAFMYTGELAKAAENGF
NKLWENRDTNNETRIAIEGIQRGLRCCGSAGPADWGLLNIPSSCCDDGVIACTVSNAHSD
GCATLLSNFVNDSGLLIAWFAIVFAGIELVGVIFACCLANSIRNANRRQYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g8185.t1 CDD cd03127 tetraspanin_LEL 106 192 2.70113E-18
9 g8185.t1 Gene3D G3DSA:1.10.1450.10 Tetraspanin 109 191 9.6E-13
2 g8185.t1 PANTHER PTHR19282 TETRASPANIN 6 225 3.8E-42
3 g8185.t1 PANTHER PTHR19282:SF471 CD63 ANTIGEN 6 225 3.8E-42
19 g8185.t1 PIRSF PIRSF002419 Tetraspanin 1 231 8.4E-48
6 g8185.t1 PRINTS PR00259 Transmembrane four family signature 12 35 1.2E-33
5 g8185.t1 PRINTS PR00259 Transmembrane four family signature 51 77 1.2E-33
4 g8185.t1 PRINTS PR00259 Transmembrane four family signature 78 106 1.2E-33
7 g8185.t1 PRINTS PR00259 Transmembrane four family signature 196 222 1.2E-33
1 g8185.t1 Pfam PF00335 Tetraspanin family 10 220 2.5E-45
10 g8185.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g8185.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
14 g8185.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 53 -
16 g8185.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 77 -
11 g8185.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 88 -
18 g8185.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 108 -
13 g8185.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 109 195 -
15 g8185.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 196 219 -
12 g8185.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 220 231 -
25 g8185.t1 ProSitePatterns PS00421 Transmembrane 4 family signature. 62 84 -
8 g8185.t1 SUPERFAMILY SSF48652 Tetraspanin 106 192 1.96E-15
24 g8185.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
21 g8185.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
23 g8185.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
22 g8185.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -

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