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 g4999 g4999.t5 TTS g4999.t5 6380330 6380330
chr_2 g4999 g4999.t5 isoform g4999.t5 6381202 6384105
chr_2 g4999 g4999.t5 exon g4999.t5.exon1 6381202 6382604
chr_2 g4999 g4999.t5 cds g4999.t5.CDS1 6382233 6382604
chr_2 g4999 g4999.t5 exon g4999.t5.exon2 6383154 6383482
chr_2 g4999 g4999.t5 cds g4999.t5.CDS2 6383154 6383219
chr_2 g4999 g4999.t5 exon g4999.t5.exon3 6383998 6384105
chr_2 g4999 g4999.t5 TSS g4999.t5 6384096 6384096

Sequences

>g4999.t5 Gene=g4999 Length=1840
GATTTACGCAAAAAAATTTATTCAACAAAATTATTTTATTCTTCACTCATATATTATCAT
TTTAATTTCATCATTCATCAAGTTTCTTTACATCAAAAGTTGTAAAAGCAGACAATACAC
ACATACAAACAGAAAAAAATATTTTTCATTCTGTTTCAACAAGTACTTTATCAACAGTAC
GAACAACGTTCATCACAAAACCAGACAAGCACGAGCACGTAAAAGAAAAGGAAAGAAAGT
TTTCATTACGCGGCAGCATTTACAATATTTATCATTCTTCGTTTTTCAACATTCGGTGCA
AGCAATAATAAACGTATTCTTGTTGTCTACTTGTCACTGTATTAATTAACATTATAAGAC
CTTGTATCATCATGGCAAAGGGATTTGGCATCAACTGCATTAAGTATCTAGTCTTCTTTT
TCAACTTTTTGTTCGCTATGACAGGACTATTAACAATTATAGTCGGCGCGATTATTCAGA
GTTCATATCATCATTATGAAAACTTTATTGGAGAATCTTTTTGGAGCGCTCCGATTATTC
TTATGATAGTGGGTTCATTAATCTTCTTCATATCATTCCTGGGATGCTGTGGAGCATTAC
GAGAATCGTCTTGTTTGATATTGACATTTTCAGTCTTCTTGCTATTTGTGTTTATCACTG
AAATTGGCATTGGTGTTGCTGGCTATATCAAACATGCTGAATTACCTGGTATTCTTGAGC
GTCAATTCAATAGAACTTTGGATGACTACACAACATCAATTGAGGCTCAACAGGCATGGA
GTTTGGTTCAAGGTGAATTGCAATGGTAAGTTTACAATAAATTTCATCATTATGTTAAAA
AGCGTTGTCCGTATTTTGTTCGTTTGTCTGTCTGTTTTCATAAAAACTTTTTCGTTCAAC
TTTTTGTAATATTCTATTACTCTCATAGGACTAGTATAGCGTAAATACCCAAACTCCTTA
TTGTTATTGAATTTTGTTATGAGAAAAGTGTTATAAAAGCTTTTTTCATCAACATTTTTT
TATTGTATAAAATTTTCATATTTTAGCATAATTTTTAATTCAAATTTATTATTCCAACTA
CAAAATTCTTACAAAAAGTTTCTAAAAATGAGGTTCAATGATGAACTCATGATCTGTCAC
AAGAAAATGTGTTATTAACATCTTTTTGATATTATTAATACTAATGAATTTTTTTAATTT
GCTAGCTGCGGAATTTATGGACCGTTAGACTGGAAACCAATTTTCAAAAACAAAACTGTA
CCATCCACATGTTGTCACATTCTTCCAGTGAACGTGAAAAATTGTGAAGTCAAATATTCA
TCTGAAGAAGGTTGCTATCAAAAGCTTTTGGATTTCCTTGATACAAAATCGTTGTTATTG
GGAGGTGTTGGTGTTGGAATAGCCATAATTCAACTTCTTGGTGTCATTTTTGCATGTGCA
CTGTCACGAGCATTCCGTGAAAATTATGAGACAGTTTAAATGCATTTATTTTTTTATTAC
ACGTACATGAGCCATGATCATCAAAATTATTATTACTAGTAGATTTAATATTGTCATAAA
GCAACAGCATTAGAGCTTACAAAGAAAACATTCCTGACAATCTCATCGCGGATTGAATTA
GAAAATTTATCGAGTCATATTATGTTGCTGAGGCTATTATATCATTAAAATTCTTTTGAA
TCTCTTTCCTATAGTATTCAGTAGCAATGTGTTGAAGTAGTGATATTAAAAACAATATAA
AAGGAAGAAAATGCTGATTGACTTGACTTTATGTTAGAATTTAAAAAAGTTCGTTTGAAT
TTATTAGAGAGTGCAAAGCAAAAAAAAAGTTCAAAAGAAA

>g4999.t5 Gene=g4999 Length=145
MAKGFGINCIKYLVFFFNFLFAMTGLLTIIVGAIIQSSYHHYENFIGESFWSAPIILMIV
GSLIFFISFLGCCGALRESSCLILTFSVFLLFVFITEIGIGVAGYIKHAELPGILERQFN
RTLDDYTTSIEAQQAWSLVQGELQW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4999.t5 PANTHER PTHR19282 TETRASPANIN 6 142 9.9E-29
3 g4999.t5 PANTHER PTHR19282:SF456 TETRASPANIN 6 142 9.9E-29
6 g4999.t5 PRINTS PR00259 Transmembrane four family signature 12 35 5.6E-26
4 g4999.t5 PRINTS PR00259 Transmembrane four family signature 50 76 5.6E-26
5 g4999.t5 PRINTS PR00259 Transmembrane four family signature 77 105 5.6E-26
1 g4999.t5 Pfam PF00335 Tetraspanin family 10 143 1.7E-29
11 g4999.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
17 g4999.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
13 g4999.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 36 54 -
16 g4999.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 55 76 -
12 g4999.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 77 82 -
15 g4999.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 83 106 -
14 g4999.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 107 145 -
10 g4999.t5 ProSitePatterns PS00421 Transmembrane 4 family signature. 61 83 -
8 g4999.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
7 g4999.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
9 g4999.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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