General information for g12873.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Peptide transporter family 1.
Parent gene
- The parent gene g12873 is located on chr_1: 26667068..26669379 (+ 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_1 | g12873 | g12873.t1 | isoform | g12873.t1 | 26667068 | 26669379 |
| chr_1 | g12873 | g12873.t1 | exon | g12873.t1.exon1 | 26667068 | 26667092 |
| chr_1 | g12873 | g12873.t1 | cds | g12873.t1.CDS1 | 26667068 | 26667092 |
| chr_1 | g12873 | g12873.t1 | exon | g12873.t1.exon2 | 26667145 | 26667711 |
| chr_1 | g12873 | g12873.t1 | cds | g12873.t1.CDS2 | 26667145 | 26667711 |
| chr_1 | g12873 | g12873.t1 | exon | g12873.t1.exon3 | 26667768 | 26668882 |
| chr_1 | g12873 | g12873.t1 | cds | g12873.t1.CDS3 | 26667768 | 26668882 |
| chr_1 | g12873 | g12873.t1 | exon | g12873.t1.exon4 | 26668942 | 26669115 |
| chr_1 | g12873 | g12873.t1 | cds | g12873.t1.CDS4 | 26668942 | 26669115 |
| chr_1 | g12873 | g12873.t1 | exon | g12873.t1.exon5 | 26669182 | 26669379 |
| chr_1 | g12873 | g12873.t1 | cds | g12873.t1.CDS5 | 26669182 | 26669379 |
| chr_1 | g12873 | g12873.t1 | TSS | g12873.t1 | NA | NA |
| chr_1 | g12873 | g12873.t1 | TTS | g12873.t1 | NA | NA |
Sequences
>g12873.t1 Gene=g12873 Length=2079
ATGGCAGCTTCAATAAAAAGTAAAGATGATCTAATTAAAAGAAGTACAACTGACATCGAA
AGCATTCAGAAAAAGTCAAAATTTCCAAAATCAGTTTTTTTCATAGTCGCCAATGAGTTT
TGTGAGCGATTCAATTACTATGGAATAAGAGCAATTTTGTCACTTTATTTGACAAGAAAA
CTTTTGCTTTCTGACGATACTGCAACTATAATTTATCATGGATTTGCAAGTCTCGTCTAC
AGTTTTTGTGTTTTGGGTGCAATCATTGCTGACTCTTTTTTGGGAAAATTTCTAACAATT
GTTTGGCTATCAATTGTTTATTTGATTGGAAATATTATTATGACTCTTGGCGCTGTTGAA
CCTTGGAAATTGCCTAATTTGGAATTTGCTATGATTGGTTTAGTACTTATTGCACTCGGA
AGTGGTGGCATCAAGCCTTGTGTTGCTGCATTTGGAGGAGAACAATTTAAATTGCCACAA
CAAGCAAAGCAATTGGCAATTTTCTTCTCAATGTTTTATTTTTCAATAAATCTTGGTTCA
TTCTTTTCGACAATTGTCACACCAATTTTGCGAGAAAATATCGTATGTTTTGGAATGATT
GATTGCTATCCACTTGGTTTTGGTTTACCTGCTGTTTTAATGAGTGTTGCAATTATTATT
TTCCTTATTGGAAAACCAATGTACAAAATTTTACCAAATCAAGGAAATATGTTTGTAAAA
GTTTGCGGTTGTATAGCAAATGCAATTTCTACAAGAGCAAAAGAAAAGAATACAAATCCA
TGTGAACATTGGCTTGATTATGCTGAAGCAAAGTATGGACGAAAACTAGTGATGGAAACA
AAAACTCTTCTCAAATTGCTCGTTCTTTATATTCCATTGCCATTATTTTGGGCACTTTAT
GATCAACAAGGTTCACGATGGACATTTCAAGCAACTCGAATGGATGGCGACTTTGGTTGG
ATTACAATTCAGCCTGATCAAATGCAAGTCATCAATCCATTGCTAATTCTCATTTTCATT
CCTCTGTGTGAAATCTTTTTATATCCAATTCTTGCACGTTTCGGAATTCGTCGTCCATTA
CAAAAAATGACACTTGGTGGAATATTGGCTGGTGTTGCTTTCCTTTGTTCAATGGTCTTG
GAAATTCATCTTGAAAAAACTTATCCACTCTTGCCATCATCGGGCGAATCACAATTGAGA
ATGTTTAATGGTGGACCATGCGCTTATGAAGTCACAACAAATCTTGAAGGAAATGCAGCA
AAGTTTGAACTTCCACCAAATTCATATTTTTCTGATCTTAAAATAAAAGTACCAGAGGAA
ACAAGAAGCTTTGAATATAAACTTAGAACACTTAATAATCCAAATTGTGCAAGTTCAGAT
GGTGTTGGATTGTTAAATAGTGGAAAAGCCAACAGTATATTTTTAAATGGAAAAAATTAT
GTCAATCAATATGTTGATGATACAGATAAGAGTAATGGCTTGGCAACTATTCGTATTTTA
GCTAGTTTACCAGCAACAAGCAATGTCGTGCTAATGCATTCCAAGAAAGGAATAATCTAT
GAGGAACCAGCAAGTTTTCATGAGCTTAAAGAAATTCCAGTTGGAAATTATAAAATTATG
GTTGACAATAAAATGATTGGAGAACATAAGATTCAAATTGGCGGTGTCTATTCAATTGTT
ATTTATGAAGTAAATCAAGGAAAATTTTCAGTAAATGTTTTCACTATCACTGAGCCAAAT
TCAATTAGCATTCTTTGGCTAATTCCTCAATATTTTTGTGTCACACTCGCTGAAGTTATG
TTTGCAGTTACAGGTTTAGAATTTTCATATACTCAAGCTCCTGAAAGTATGAAATCAGTC
TTACAAGGCTGTTGGCAAATGACTGTTGGATTGGGAAATTTAATTGTGGCTATTGTCGTT
ACAACAAAAATGTTCGAGTCACAAGCTTTCGAATTTTTGTTGTTTGCACTAATGATGTTC
CTTGATATGGCTATATTTATGGTTCTTGGAATTTATTACAAACCAATTCCACTAGAAGAA
CTCAAGAAGGTTGAAAATGAAAGCAATGAGAAGAAATAA
>g12873.t1 Gene=g12873 Length=692
MAASIKSKDDLIKRSTTDIESIQKKSKFPKSVFFIVANEFCERFNYYGIRAILSLYLTRK
LLLSDDTATIIYHGFASLVYSFCVLGAIIADSFLGKFLTIVWLSIVYLIGNIIMTLGAVE
PWKLPNLEFAMIGLVLIALGSGGIKPCVAAFGGEQFKLPQQAKQLAIFFSMFYFSINLGS
FFSTIVTPILRENIVCFGMIDCYPLGFGLPAVLMSVAIIIFLIGKPMYKILPNQGNMFVK
VCGCIANAISTRAKEKNTNPCEHWLDYAEAKYGRKLVMETKTLLKLLVLYIPLPLFWALY
DQQGSRWTFQATRMDGDFGWITIQPDQMQVINPLLILIFIPLCEIFLYPILARFGIRRPL
QKMTLGGILAGVAFLCSMVLEIHLEKTYPLLPSSGESQLRMFNGGPCAYEVTTNLEGNAA
KFELPPNSYFSDLKIKVPEETRSFEYKLRTLNNPNCASSDGVGLLNSGKANSIFLNGKNY
VNQYVDDTDKSNGLATIRILASLPATSNVVLMHSKKGIIYEEPASFHELKEIPVGNYKIM
VDNKMIGEHKIQIGGVYSIVIYEVNQGKFSVNVFTITEPNSISILWLIPQYFCVTLAEVM
FAVTGLEFSYTQAPESMKSVLQGCWQMTVGLGNLIVAIVVTTKMFESQAFEFLLFALMMF
LDMAIFMVLGIYYKPIPLEELKKVENESNEKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 31 | g12873.t1 | CDD | cd17347 | MFS_SLC15A1_2_like | 29 | 677 | 4.39393E-177 |
| 7 | g12873.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 5 | 402 | 3.6E-114 |
| 6 | g12873.t1 | Gene3D | G3DSA:1.20.1250.20 | MFS general substrate transporter like domains | 548 | 677 | 1.2E-25 |
| 3 | g12873.t1 | PANTHER | PTHR11654 | OLIGOPEPTIDE TRANSPORTER-RELATED | 24 | 679 | 1.4E-227 |
| 4 | g12873.t1 | PANTHER | PTHR11654:SF465 | - | 24 | 679 | 1.4E-227 |
| 1 | g12873.t1 | Pfam | PF00854 | POT family | 97 | 404 | 3.1E-92 |
| 2 | g12873.t1 | Pfam | PF00854 | POT family | 568 | 642 | 3.2E-12 |
| 19 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 69 | - |
| 30 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 90 | - |
| 13 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 91 | 96 | - |
| 21 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 119 | - |
| 14 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 120 | 130 | - |
| 26 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 153 | - |
| 10 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 154 | 164 | - |
| 29 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 185 | - |
| 15 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 204 | - |
| 23 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 205 | 224 | - |
| 11 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 225 | 282 | - |
| 28 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 300 | - |
| 18 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 301 | 329 | - |
| 24 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 330 | 351 | - |
| 9 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 352 | 362 | - |
| 27 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 363 | 384 | - |
| 16 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 385 | 583 | - |
| 22 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 584 | 608 | - |
| 12 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 609 | 619 | - |
| 20 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 620 | 640 | - |
| 17 | g12873.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 641 | 651 | - |
| 25 | g12873.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 652 | 673 | - |
| 8 | g12873.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 674 | 692 | - |
| 43 | g12873.t1 | ProSitePatterns | PS01022 | PTR2 family proton/oligopeptide symporters signature 1. | 86 | 110 | - |
| 44 | g12873.t1 | ProSitePatterns | PS01023 | PTR2 family proton/oligopeptide symporters signature 2. | 169 | 181 | - |
| 5 | g12873.t1 | SUPERFAMILY | SSF103473 | MFS general substrate transporter | 19 | 380 | 3.53E-17 |
| 41 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 90 | - |
| 33 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 97 | 119 | - |
| 38 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 130 | 152 | - |
| 37 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 187 | - |
| 39 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
| 42 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 300 | - |
| 35 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 330 | 352 | - |
| 32 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 384 | - |
| 34 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 584 | 606 | - |
| 36 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 619 | 641 | - |
| 40 | g12873.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 651 | 673 | - |
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:0016020 | membrane | CC |
| GO:0055085 | transmembrane transport | BP |
| GO:0006857 | oligopeptide transport | BP |
| GO:0022857 | transmembrane transporter activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14206 (solute carrier family 15 (oligopeptide transporter), member 1)
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