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.t30 isoform g8185.t30 28961709 28963725
chr_2 g8185 g8185.t30 exon g8185.t30.exon1 28961709 28962247
chr_2 g8185 g8185.t30 TTS g8185.t30 28961757 28961757
chr_2 g8185 g8185.t30 cds g8185.t30.CDS1 28962204 28962247
chr_2 g8185 g8185.t30 exon g8185.t30.exon2 28962309 28962702
chr_2 g8185 g8185.t30 cds g8185.t30.CDS2 28962309 28962702
chr_2 g8185 g8185.t30 exon g8185.t30.exon3 28962761 28962952
chr_2 g8185 g8185.t30 cds g8185.t30.CDS3 28962761 28962952
chr_2 g8185 g8185.t30 exon g8185.t30.exon4 28963542 28963621
chr_2 g8185 g8185.t30 cds g8185.t30.CDS4 28963542 28963568
chr_2 g8185 g8185.t30 exon g8185.t30.exon5 28963700 28963725
chr_2 g8185 g8185.t30 TSS g8185.t30 28963786 28963786

Sequences

>g8185.t30 Gene=g8185 Length=1231
TAATATTTTTCTACCTAGTGAGCTCAAAATAAATAAAAAAGAAATATGGGTTTAACTTGT
GGAGCATCTGTGGTCAAATATGGCATTTTTATTTTCAACCTTCTTTGTTGCTGGTATAGC
ATTGATCGTTGTTGGTGCAATTCCACTATTCAAACTTGATGACATTCGAGATGCCTTTCC
TGAAAACAATCCAGCCACTGTTCCCATCATAATCGTCGTTCTTGGCTCGATAATCTTTAT
CATCAGTTTCTTTGGATGTTGTGGAGCTATTAGAGAAAATCAGTGTATGGTTTCAACGTA
CGCATTTTTCCTACTCATATTGGTCGTTCTTCAAATTGTTATCGCCGTTTTCGCATTTAT
GTATACAGGTGAACTTGCGAAAGCTGCAGAAAATGGTTTCAATAAATTATGGGAAAACAG
AGACACAAATAATGAAACAAGAATTGCTATCGAAGGCATACAACGCGGACTTCGCTGTTG
TGGTTCAGCTGGACCCGCTGATTGGGGATTATTAAATATTCCATCTTCATGCTGTGATGA
TGGAGTTATAGCATGCACAGTGTCGAACGCTCATTCAGATGGATGTGCTACACTTCTTTC
CAACTTTGTCAATGATAGTGGACTCTTGATTGCATGGTTTGCAATTGTCTTTGCTGGTAT
TGAACTTGTTGGTGTAATCTTCGCCTGTTGTCTGGCCAATTCAATTCGAAATGCAAACAG
AAGACAATATGCATAAAAGTCTACAATGTACTAATTTAATAGAAATAGGAATTTGAAACC
AAATTTTTTTTGTTTAAAAATCTATTCTTATATATCTCTAATTAATTTTATAGTACAGCT
ATAGATTGATGTCAAGAAAATAAGTTTTTTTTTCACTTATTTATCGCTATTAATTGATAA
GTAAGTTGAATACATATGTGTGTGTGTCACCATTTCTTTGGTCTATCATCTATATCAATT
CTAATTTATCAATCTTAAGTTTCTGTGTGAGCTAGGCACGGCAGATAAGGGTCACTTCTA
TATATGCAAGAGAAAAGAAAACACGCCAACAAGAAATATTTTATTTTTATTTTAGTCTTT
TAAAATATGTTATCGTAAAAATTGTATATTTTTTATTCTTTAAATGTTGTACTTTGAACA
CAAGTTGTTAATAAACAAAGTAAAAGTGATTAGTTCTTGAATAAATGCTTTAAATATCAA
CAATTCAAAATTTAATGGTAAATAATAATTT

>g8185.t30 Gene=g8185 Length=218
MAFLFSTFFVAGIALIVVGAIPLFKLDDIRDAFPENNPATVPIIIVVLGSIIFIISFFGC
CGAIRENQCMVSTYAFFLLILVVLQIVIAVFAFMYTGELAKAAENGFNKLWENRDTNNET
RIAIEGIQRGLRCCGSAGPADWGLLNIPSSCCDDGVIACTVSNAHSDGCATLLSNFVNDS
GLLIAWFAIVFAGIELVGVIFACCLANSIRNANRRQYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g8185.t30 CDD cd03127 tetraspanin_LEL 93 179 1.21548E-18
8 g8185.t30 Gene3D G3DSA:1.10.1450.10 Tetraspanin 96 178 8.5E-13
2 g8185.t30 PANTHER PTHR19282 TETRASPANIN 3 212 3.5E-39
3 g8185.t30 PANTHER PTHR19282:SF471 CD63 ANTIGEN 3 212 3.5E-39
20 g8185.t30 PIRSF PIRSF002419 Tetraspanin 1 218 8.7E-43
6 g8185.t30 PRINTS PR00259 Transmembrane four family signature 38 64 2.6E-28
4 g8185.t30 PRINTS PR00259 Transmembrane four family signature 65 93 2.6E-28
5 g8185.t30 PRINTS PR00259 Transmembrane four family signature 183 209 2.6E-28
1 g8185.t30 Pfam PF00335 Tetraspanin family 3 207 1.5E-41
13 g8185.t30 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
14 g8185.t30 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
15 g8185.t30 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 15 -
19 g8185.t30 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 19 -
11 g8185.t30 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 42 -
17 g8185.t30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 64 -
9 g8185.t30 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 65 75 -
18 g8185.t30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 95 -
12 g8185.t30 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 96 182 -
16 g8185.t30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 183 206 -
10 g8185.t30 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 218 -
26 g8185.t30 ProSitePatterns PS00421 Transmembrane 4 family signature. 49 71 -
7 g8185.t30 SUPERFAMILY SSF48652 Tetraspanin 93 179 1.83E-15
25 g8185.t30 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 2 24 -
23 g8185.t30 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 39 61 -
24 g8185.t30 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -
22 g8185.t30 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -

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