General information for g16139.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lysosomal-associated transmembrane protein 4A.
Parent gene
- The parent gene g16139 is located on chr_4: 8347982..8349062 (- strand)
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.t1 | TTS | g16139.t1 | 8347883 | 8347883 |
| chr_4 | g16139 | g16139.t1 | isoform | g16139.t1 | 8347982 | 8349062 |
| chr_4 | g16139 | g16139.t1 | exon | g16139.t1.exon1 | 8347982 | 8348074 |
| chr_4 | g16139 | g16139.t1 | cds | g16139.t1.CDS1 | 8347982 | 8348074 |
| chr_4 | g16139 | g16139.t1 | exon | g16139.t1.exon2 | 8348129 | 8348265 |
| chr_4 | g16139 | g16139.t1 | cds | g16139.t1.CDS2 | 8348129 | 8348265 |
| chr_4 | g16139 | g16139.t1 | exon | g16139.t1.exon3 | 8348319 | 8348613 |
| chr_4 | g16139 | g16139.t1 | cds | g16139.t1.CDS3 | 8348319 | 8348613 |
| chr_4 | g16139 | g16139.t1 | exon | g16139.t1.exon4 | 8348733 | 8348912 |
| chr_4 | g16139 | g16139.t1 | cds | g16139.t1.CDS4 | 8348733 | 8348912 |
| chr_4 | g16139 | g16139.t1 | exon | g16139.t1.exon5 | 8348973 | 8349062 |
| chr_4 | g16139 | g16139.t1 | cds | g16139.t1.CDS5 | 8348973 | 8349062 |
| chr_4 | g16139 | g16139.t1 | TSS | g16139.t1 | 8349120 | 8349120 |
Sequences
>g16139.t1 Gene=g16139 Length=795
ATGAATAATTTGGAATCAAATAAATATCGATGTTTCTTTAATTTAGTTCATGTCAAAACA
TTCACAATTTTCATTGGAGGATGGCATATGGTCCTAAATCTTTCTTGTATTATTTTACTT
ATGGTAATATCACGTAATCCAGCAGTTACAGAATTTTCTTATGATTCAAGTGCTGATGAA
GATGACATTTTACCAACACCAGTTTCAAATAAAATTGGTGAAGTGCAACAATATAGAGAA
CATTCATTGACTTATGGCGACATTGATATGGGTGGATTTGTATGTCTTTGCATGCTGATT
ATAACATTCCTTTTAATTTATGGATGTATCAAAGAAAAACCTGGCCATTTACTACCATTT
TTCTTTCTTCAATTATGTGATTTTGCCATAACATCATTGAGTGCTGCTGGTTATTTGTGC
TATTTAAAGACAGTCAAAACTTTAATTCAAGAATCAAATCGTTTGCCATGGAAAGAAGAT
ATAATTAAAATTGATTCACAAACTTTGAGTGTAATGGTCCTTGTAATTTTTGTTTTCATG
GTCATTTTAAAAGCTTATTGTATTGGTATTGTTTGGAGATGCTATAAATATTTAACAATT
CGAAAGAGTACAACACTTTTGTCATTTATTATTCAAGAACCAACAATGAATCAAGATGCA
AATTGTGGATCTCTTTTACCTGGCTATGAAGAGGCTTTAAATATGAAAATGGCACCACCA
AGTTATTCTGCTGCTATGGAAATGCAACAAGAAATTTCACCACCAGCATACCAAGAATTA
CAACGTTCCAATTAA
>g16139.t1 Gene=g16139 Length=264
MNNLESNKYRCFFNLVHVKTFTIFIGGWHMVLNLSCIILLMVISRNPAVTEFSYDSSADE
DDILPTPVSNKIGEVQQYREHSLTYGDIDMGGFVCLCMLIITFLLIYGCIKEKPGHLLPF
FFLQLCDFAITSLSAAGYLCYLKTVKTLIQESNRLPWKEDIIKIDSQTLSVMVLVIFVFM
VILKAYCIGIVWRCYKYLTIRKSTTLLSFIIQEPTMNQDANCGSLLPGYEEALNMKMAPP
SYSAAMEMQQEISPPAYQELQRSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g16139.t1 | PANTHER | PTHR12479 | LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN | 5 | 259 | 4.4E-67 |
| 3 | g16139.t1 | PANTHER | PTHR12479:SF10 | LYSOSOMAL-ASSOCIATED TRANSMEMBRANE PROTEIN | 5 | 259 | 4.4E-67 |
| 1 | g16139.t1 | Pfam | PF03821 | Golgi 4-transmembrane spanning transporter | 149 | 243 | 4.8E-11 |
| 8 | g16139.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 20 | - |
| 16 | g16139.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 11 | g16139.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 44 | 89 | - |
| 13 | g16139.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 110 | - |
| 9 | g16139.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 111 | 116 | - |
| 15 | g16139.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 139 | - |
| 12 | g16139.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 140 | 168 | - |
| 14 | g16139.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 169 | 192 | - |
| 10 | g16139.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 193 | 264 | - |
| 6 | g16139.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 5 | g16139.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 88 | 110 | - |
| 4 | g16139.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 117 | 139 | - |
| 7 | g16139.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 192 | - |
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 transcript has been annotated with K12387 (lysosomal-associated transmembrane protein)
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.
