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.t17 isoform g8185.t17 28961709 28963602
chr_2 g8185 g8185.t17 exon g8185.t17.exon1 28961709 28962247
chr_2 g8185 g8185.t17 TTS g8185.t17 28961757 28961757
chr_2 g8185 g8185.t17 cds g8185.t17.CDS1 28962204 28962247
chr_2 g8185 g8185.t17 exon g8185.t17.exon2 28962309 28962702
chr_2 g8185 g8185.t17 cds g8185.t17.CDS2 28962309 28962702
chr_2 g8185 g8185.t17 exon g8185.t17.exon3 28962761 28962939
chr_2 g8185 g8185.t17 cds g8185.t17.CDS3 28962761 28962939
chr_2 g8185 g8185.t17 exon g8185.t17.exon4 28963533 28963602
chr_2 g8185 g8185.t17 cds g8185.t17.CDS4 28963533 28963602
chr_2 g8185 g8185.t17 TSS g8185.t17 28963786 28963786

Sequences

>g8185.t17 Gene=g8185 Length=1182
ATGGGTTTAACTTGTGGAGCATCTGTGGTCAAATATGGCATTTTTATTTTCAACCTTCTT
TGTGCTGTAACATTGATCGTTGTTGGTGCAATTCCACTATTCAAACTTGATGACATTCGA
GATGCCTTTCCTGAAAACAATCCAGCCACTGTTCCCATCATAATCGTCGTTCTTGGCTCG
ATAATCTTTATCATCAGTTTCTTTGGATGTTGTGGAGCTATTAGAGAAAATCAGTGTATG
GTTTCAACGTACGCATTTTTCCTACTCATATTGGTCGTTCTTCAAATTGTTATCGCCGTT
TTCGCATTTATGTATACAGGTGAACTTGCGAAAGCTGCAGAAAATGGTTTCAATAAATTA
TGGGAAAACAGAGACACAAATAATGAAACAAGAATTGCTATCGAAGGCATACAACGCGGA
CTTCGCTGTTGTGGTTCAGCTGGACCCGCTGATTGGGGATTATTAAATATTCCATCTTCA
TGCTGTGATGATGGAGTTATAGCATGCACAGTGTCGAACGCTCATTCAGATGGATGTGCT
ACACTTCTTTCCAACTTTGTCAATGATAGTGGACTCTTGATTGCATGGTTTGCAATTGTC
TTTGCTGGTATTGAACTTGTTGGTGTAATCTTCGCCTGTTGTCTGGCCAATTCAATTCGA
AATGCAAACAGAAGACAATATGCATAAAAGTCTACAATGTACTAATTTAATAGAAATAGG
AATTTGAAACCAAATTTTTTTTGTTTAAAAATCTATTCTTATATATCTCTAATTAATTTT
ATAGTACAGCTATAGATTGATGTCAAGAAAATAAGTTTTTTTTTCACTTATTTATCGCTA
TTAATTGATAAGTAAGTTGAATACATATGTGTGTGTGTCACCATTTCTTTGGTCTATCAT
CTATATCAATTCTAATTTATCAATCTTAAGTTTCTGTGTGAGCTAGGCACGGCAGATAAG
GGTCACTTCTATATATGCAAGAGAAAAGAAAACACGCCAACAAGAAATATTTTATTTTTA
TTTTAGTCTTTTAAAATATGTTATCGTAAAAATTGTATATTTTTTATTCTTTAAATGTTG
TACTTTGAACACAAGTTGTTAATAAACAAAGTAAAAGTGATTAGTTCTTGAATAAATGCT
TTAAATATCAACAATTCAAAATTTAATGGTAAATAATAATTT

>g8185.t17 Gene=g8185 Length=228
MGLTCGASVVKYGIFIFNLLCAVTLIVVGAIPLFKLDDIRDAFPENNPATVPIIIVVLGS
IIFIISFFGCCGAIRENQCMVSTYAFFLLILVVLQIVIAVFAFMYTGELAKAAENGFNKL
WENRDTNNETRIAIEGIQRGLRCCGSAGPADWGLLNIPSSCCDDGVIACTVSNAHSDGCA
TLLSNFVNDSGLLIAWFAIVFAGIELVGVIFACCLANSIRNANRRQYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g8185.t17 CDD cd03127 tetraspanin_LEL 103 189 4.0043E-18
9 g8185.t17 Gene3D G3DSA:1.10.1450.10 Tetraspanin 106 188 9.4E-13
2 g8185.t17 PANTHER PTHR19282 TETRASPANIN 6 222 3.6E-40
3 g8185.t17 PANTHER PTHR19282:SF471 CD63 ANTIGEN 6 222 3.6E-40
19 g8185.t17 PIRSF PIRSF002419 Tetraspanin 1 228 2.7E-44
7 g8185.t17 PRINTS PR00259 Transmembrane four family signature 12 35 1.6E-30
5 g8185.t17 PRINTS PR00259 Transmembrane four family signature 48 74 1.6E-30
6 g8185.t17 PRINTS PR00259 Transmembrane four family signature 75 103 1.6E-30
4 g8185.t17 PRINTS PR00259 Transmembrane four family signature 193 219 1.6E-30
1 g8185.t17 Pfam PF00335 Tetraspanin family 10 217 2.3E-41
10 g8185.t17 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
16 g8185.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
14 g8185.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 52 -
15 g8185.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 74 -
12 g8185.t17 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 75 85 -
17 g8185.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -
13 g8185.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 192 -
18 g8185.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 193 216 -
11 g8185.t17 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 217 228 -
25 g8185.t17 ProSitePatterns PS00421 Transmembrane 4 family signature. 59 81 -
8 g8185.t17 SUPERFAMILY SSF48652 Tetraspanin 103 189 1.96E-15
24 g8185.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
22 g8185.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 49 71 -
23 g8185.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -
21 g8185.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 193 215 -

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