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.t3 TTS g16139.t3 8347883 8347883
chr_4 g16139 g16139.t3 isoform g16139.t3 8347982 8348612
chr_4 g16139 g16139.t3 exon g16139.t3.exon1 8347982 8348074
chr_4 g16139 g16139.t3 cds g16139.t3.CDS1 8347982 8348074
chr_4 g16139 g16139.t3 exon g16139.t3.exon2 8348129 8348222
chr_4 g16139 g16139.t3 cds g16139.t3.CDS2 8348129 8348222
chr_4 g16139 g16139.t3 exon g16139.t3.exon3 8348303 8348612
chr_4 g16139 g16139.t3 cds g16139.t3.CDS3 8348303 8348592
chr_4 g16139 g16139.t3 TSS g16139.t3 8349120 8349120

Sequences

>g16139.t3 Gene=g16139 Length=497
GTGGATTTGTATGTCTTTGCATGCTGATTATAACATTCCTTTTAATTTATGGATGTATCA
AAGAAAAACCTGGCCATTTACTACCATTTTTCTTTCTTCAATTATGTGATTTTGCCATAA
CATCATTGAGTGCTGCTGGTTATTTGTGCTATTTAAAGACAGTCAAAACTTTAATTCAAG
AATCAAATCGTTTGCCATGGAAAGAAGATATAATTAAAATTGATTCACAAACTTTGAGTG
TAATGGTCCTTGTAATTTTTGTTTTCATGGTCATTTTAAAAGCTTATTGTATTGGTAAGA
ATAAGAAAATTACAACACTTTTGTCATTTATTATTCAAGAACCAACAATGAATCAAGATG
CAAATTGTGGATCTCTTTTACCTGGCTATGAAGAGGCTTTAAATATGAAAATGGCACCAC
CAAGTTATTCTGCTGCTATGGAAATGCAACAAGAAATTTCACCACCAGCATACCAAGAAT
TACAACGTTCCAATTAA

>g16139.t3 Gene=g16139 Length=158
MLIITFLLIYGCIKEKPGHLLPFFFLQLCDFAITSLSAAGYLCYLKTVKTLIQESNRLPW
KEDIIKIDSQTLSVMVLVIFVFMVILKAYCIGKNKKITTLLSFIIQEPTMNQDANCGSLL
PGYEEALNMKMAPPSYSAAMEMQQEISPPAYQELQRSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g16139.t3 PANTHER PTHR12479 LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN 1 154 2.4E-31
2 g16139.t3 PANTHER PTHR12479:SF10 LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN 1 154 2.4E-31
8 g16139.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 14 -
9 g16139.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
10 g16139.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 9 -
13 g16139.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 10 14 -
7 g16139.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 15 23 -
11 g16139.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 24 44 -
5 g16139.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 45 64 -
12 g16139.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 65 86 -
6 g16139.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 87 158 -
3 g16139.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
4 g16139.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 69 91 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed