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_4 g16139 g16139.t4 TTS g16139.t4 8347883 8347883
chr_4 g16139 g16139.t4 isoform g16139.t4 8347982 8349062
chr_4 g16139 g16139.t4 exon g16139.t4.exon1 8347982 8348074
chr_4 g16139 g16139.t4 cds g16139.t4.CDS1 8347982 8348074
chr_4 g16139 g16139.t4 exon g16139.t4.exon2 8348129 8348265
chr_4 g16139 g16139.t4 cds g16139.t4.CDS2 8348129 8348265
chr_4 g16139 g16139.t4 exon g16139.t4.exon3 8348319 8348613
chr_4 g16139 g16139.t4 cds g16139.t4.CDS3 8348319 8348592
chr_4 g16139 g16139.t4 exon g16139.t4.exon4 8348729 8348912
chr_4 g16139 g16139.t4 exon g16139.t4.exon5 8348973 8349062
chr_4 g16139 g16139.t4 TSS g16139.t4 8349120 8349120

Sequences

>g16139.t4 Gene=g16139 Length=799
ATGAATAATTTGGAATCAAATAAATATCGATGTTTCTTTAATTTAGTTCATGTCAAAACA
TTCACAATTTTCATTGGAGGATGGCATATGGTCCTAAATCTTTCTTGTATTATTTTACTT
ATGGTAATATCACGTAATCCAGCAGTTACAGAATTTTCTTATGATTCAAGTGCTGATGAA
GATGACATTTTACCAACACCAGTTTCAAATAAAATTGGTGAAGTGCAACAATATAGAGAA
CATTCATTGACTTATGGCGACATTGATATGGTGAGGTGGATTTGTATGTCTTTGCATGCT
GATTATAACATTCCTTTTAATTTATGGATGTATCAAAGAAAAACCTGGCCATTTACTACC
ATTTTTCTTTCTTCAATTATGTGATTTTGCCATAACATCATTGAGTGCTGCTGGTTATTT
GTGCTATTTAAAGACAGTCAAAACTTTAATTCAAGAATCAAATCGTTTGCCATGGAAAGA
AGATATAATTAAAATTGATTCACAAACTTTGAGTGTAATGGTCCTTGTAATTTTTGTTTT
CATGGTCATTTTAAAAGCTTATTGTATTGGTATTGTTTGGAGATGCTATAAATATTTAAC
AATTCGAAAGAGTACAACACTTTTGTCATTTATTATTCAAGAACCAACAATGAATCAAGA
TGCAAATTGTGGATCTCTTTTACCTGGCTATGAAGAGGCTTTAAATATGAAAATGGCACC
ACCAAGTTATTCTGCTGCTATGGAAATGCAACAAGAAATTTCACCACCAGCATACCAAGA
ATTACAACGTTCCAATTAA

>g16139.t4 Gene=g16139 Length=167
MLIITFLLIYGCIKEKPGHLLPFFFLQLCDFAITSLSAAGYLCYLKTVKTLIQESNRLPW
KEDIIKIDSQTLSVMVLVIFVFMVILKAYCIGIVWRCYKYLTIRKSTTLLSFIIQEPTMN
QDANCGSLLPGYEEALNMKMAPPSYSAAMEMQQEISPPAYQELQRSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g16139.t4 PANTHER PTHR12479 LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN 1 162 1.7E-47
3 g16139.t4 PANTHER PTHR12479:SF10 LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN 1 162 1.7E-47
1 g16139.t4 Pfam PF03821 Golgi 4-transmembrane spanning transporter 52 146 2.2E-11
9 g16139.t4 Phobius SIGNAL_PEPTIDE Signal peptide region 1 14 -
10 g16139.t4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
11 g16139.t4 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 9 -
14 g16139.t4 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 10 14 -
8 g16139.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 15 23 -
13 g16139.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 45 -
6 g16139.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 46 73 -
12 g16139.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 74 95 -
7 g16139.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 96 167 -
4 g16139.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
5 g16139.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -

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