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.t41 TTS g8185.t41 28961757 28961757
chr_2 g8185 g8185.t41 isoform g8185.t41 28961822 28963602
chr_2 g8185 g8185.t41 exon g8185.t41.exon1 28961822 28962247
chr_2 g8185 g8185.t41 cds g8185.t41.CDS1 28962204 28962247
chr_2 g8185 g8185.t41 exon g8185.t41.exon2 28962309 28962702
chr_2 g8185 g8185.t41 cds g8185.t41.CDS2 28962309 28962702
chr_2 g8185 g8185.t41 exon g8185.t41.exon3 28962761 28962952
chr_2 g8185 g8185.t41 cds g8185.t41.CDS3 28962761 28962952
chr_2 g8185 g8185.t41 exon g8185.t41.exon4 28963528 28963602
chr_2 g8185 g8185.t41 cds g8185.t41.CDS4 28963528 28963602
chr_2 g8185 g8185.t41 TSS g8185.t41 28963786 28963786

Sequences

>g8185.t41 Gene=g8185 Length=1087
ATGGGTTTAACTTGTGGAGCATCTGTGGTCAAATATGGCATTTTTATTTTCAACCTTCTT
TGTGCTGTAAGTAAAGTTGCTGGTATAGCATTGATCGTTGTTGGTGCAATTCCACTATTC
AAACTTGATGACATTCGAGATGCCTTTCCTGAAAACAATCCAGCCACTGTTCCCATCATA
ATCGTCGTTCTTGGCTCGATAATCTTTATCATCAGTTTCTTTGGATGTTGTGGAGCTATT
AGAGAAAATCAGTGTATGGTTTCAACGTACGCATTTTTCCTACTCATATTGGTCGTTCTT
CAAATTGTTATCGCCGTTTTCGCATTTATGTATACAGGTGAACTTGCGAAAGCTGCAGAA
AATGGTTTCAATAAATTATGGGAAAACAGAGACACAAATAATGAAACAAGAATTGCTATC
GAAGGCATACAACGCGGACTTCGCTGTTGTGGTTCAGCTGGACCCGCTGATTGGGGATTA
TTAAATATTCCATCTTCATGCTGTGATGATGGAGTTATAGCATGCACAGTGTCGAACGCT
CATTCAGATGGATGTGCTACACTTCTTTCCAACTTTGTCAATGATAGTGGACTCTTGATT
GCATGGTTTGCAATTGTCTTTGCTGGTATTGAACTTGTTGGTGTAATCTTCGCCTGTTGT
CTGGCCAATTCAATTCGAAATGCAAACAGAAGACAATATGCATAAAAGTCTACAATGTAC
TAATTTAATAGAAATAGGAATTTGAAACCAAATTTTTTTTGTTTAAAAATCTATTCTTAT
ATATCTCTAATTAATTTTATAGTACAGCTATAGATTGATGTCAAGAAAATAAGTTTTTTT
TTCACTTATTTATCGCTATTAATTGATAAGTAAGTTGAATACATATGTGTGTGTGTCACC
ATTTCTTTGGTCTATCATCTATATCAATTCTAATTTATCAATCTTAAGTTTCTGTGTGAG
CTAGGCACGGCAGATAAGGGTCACTTCTATATATGCAAGAGAAAAGAAAACACGCCAACA
AGAAATATTTTATTTTTATTTTAGTCTTTTAAAATATGTTATCGTAAAAATTGTATATTT
TTTATTC

>g8185.t41 Gene=g8185 Length=234
MGLTCGASVVKYGIFIFNLLCAVSKVAGIALIVVGAIPLFKLDDIRDAFPENNPATVPII
IVVLGSIIFIISFFGCCGAIRENQCMVSTYAFFLLILVVLQIVIAVFAFMYTGELAKAAE
NGFNKLWENRDTNNETRIAIEGIQRGLRCCGSAGPADWGLLNIPSSCCDDGVIACTVSNA
HSDGCATLLSNFVNDSGLLIAWFAIVFAGIELVGVIFACCLANSIRNANRRQYA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g8185.t41 CDD cd03127 tetraspanin_LEL 109 195 2.63424E-18
9 g8185.t41 Gene3D G3DSA:1.10.1450.10 Tetraspanin 112 194 9.9E-13
2 g8185.t41 PANTHER PTHR19282 TETRASPANIN 6 228 4.3E-40
3 g8185.t41 PANTHER PTHR19282:SF471 CD63 ANTIGEN 6 228 4.3E-40
19 g8185.t41 PIRSF PIRSF002419 Tetraspanin 1 234 2.8E-45
5 g8185.t41 PRINTS PR00259 Transmembrane four family signature 12 35 1.1E-29
7 g8185.t41 PRINTS PR00259 Transmembrane four family signature 54 80 1.1E-29
6 g8185.t41 PRINTS PR00259 Transmembrane four family signature 81 109 1.1E-29
4 g8185.t41 PRINTS PR00259 Transmembrane four family signature 199 225 1.1E-29
1 g8185.t41 Pfam PF00335 Tetraspanin family 10 223 1.6E-42
10 g8185.t41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g8185.t41 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 37 -
14 g8185.t41 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 38 56 -
15 g8185.t41 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 80 -
11 g8185.t41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 81 91 -
16 g8185.t41 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 111 -
13 g8185.t41 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 112 198 -
18 g8185.t41 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 199 222 -
12 g8185.t41 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 223 234 -
25 g8185.t41 ProSitePatterns PS00421 Transmembrane 4 family signature. 65 87 -
8 g8185.t41 SUPERFAMILY SSF48652 Tetraspanin 109 195 2.09E-15
24 g8185.t41 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
21 g8185.t41 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
23 g8185.t41 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 90 112 -
22 g8185.t41 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 199 221 -

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