General information for g5704.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium-dependent serotonin transporter.
Parent gene
- The parent gene g5704 is located on chr_2: 11322287..11327265 (+ 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_2 | g5704 | g5704.t1 | isoform | g5704.t1 | 11322287 | 11327265 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon1 | 11322287 | 11322614 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS1 | 11322287 | 11322614 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon2 | 11322708 | 11322720 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS2 | 11322708 | 11322720 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon3 | 11322930 | 11323008 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS3 | 11322930 | 11323008 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon4 | 11323095 | 11323182 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS4 | 11323095 | 11323182 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon5 | 11324939 | 11324982 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS5 | 11324939 | 11324982 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon6 | 11325047 | 11325213 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS6 | 11325047 | 11325213 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon7 | 11325282 | 11325824 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS7 | 11325282 | 11325824 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon8 | 11325877 | 11326081 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS8 | 11325877 | 11326081 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon9 | 11326614 | 11326656 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS9 | 11326614 | 11326656 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon10 | 11326718 | 11326875 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS10 | 11326718 | 11326875 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon11 | 11326949 | 11327116 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS11 | 11326949 | 11327116 |
| chr_2 | g5704 | g5704.t1 | exon | g5704.t1.exon12 | 11327188 | 11327265 |
| chr_2 | g5704 | g5704.t1 | cds | g5704.t1.CDS12 | 11327188 | 11327265 |
| chr_2 | g5704 | g5704.t1 | TSS | g5704.t1 | NA | NA |
| chr_2 | g5704 | g5704.t1 | TTS | g5704.t1 | NA | NA |
Sequences
>g5704.t1 Gene=g5704 Length=1914
ATGACAAATGAAAATTCACTTGACGCGGCCGAGTCCACGACAAATTTAACATCACCAGCA
AAGGGAAAAATTCAGCAAATCAATCATAGCGAGAAAAAAGGCAATGGTGAGGATTTGGCA
GCGGATGGTTATGATACGTGGAATGATGAAAGGAAAGAAGAAGAAAAGGAGAGCAATCCA
TTAAATCCAAATGGATCTAGTAATGCCAAAGATAAAGATCGTGAAGAGAGAGCTCTCATA
GTAAGTTTGACGCAGGGAAGACCCCGAGAGACATGGAATCAAAAAGTTGAATTTTTGCTC
GCTGTTATTGGTTTTGCCGTCGATTTAGGCAACGTGTGGCGATTTCCTTATATTTGTTAT
CAAAATGGAGGTGGAGCTTTTCTTATTCCTTACGTCATTATGTTGCTTCTTGGTGGATTG
CCGCTCTTTTATATGGAGTTAGCACTTGGACAATTTCACCGATGTGGTTGCTTATCCATT
TGGAATCGAATTTGTCCTGCATTAAAAGGTGTTGGTATGGCAATTTGCATTATAGACATT
TATATGGGAATGTATTACAACACAATTATTGGATGGGCTGTTTATTATTTCTTTGCATCA
TTTACATCTGAACTTCCTTGGGAAAAATGCGGAAAACCTTGGAATACCGAAGCATGTCTT
TCTGTCGATATACCAACAAACTTGACAAACACTACAACACCAGCGCGAGAGTATTTCGAA
CGAAATGTTCTTGAACAATACAAATCCAATGGTTTAGAATATATGGGACCAGTAAAGCCA
TCGCTTGCGCTATGTGTATTTGGCGTTTTTGTTCTAGTTTATTTTTCACTTTGGAAAGGT
GTAAAGAGTACAGGAAAGGCAGTTTGGATAACAGCACTTGCACCTTATTTTGTTCTTGTT
GTTCTTCTTATTCGTGGTGTGACATTAGATGGAGCAGGCGAAGGAATCCGTTATTATTTG
ACACCTGAATGGGAAAAATTAAAGAATACAAAAGTTTGGATTGATGCTGCATCACAAATT
TTCTTCTCTTTAGGTCCTGGTTTTGGAACATTACTTGCACTTTCAAGTTACAATAAATTC
AATAACAATTGCTATCGTGATGCTCTTCTTACAAGTTCAATCAATTGCCTGACAAGCTTT
CTTGCTGGTTTTGTAATTTTCTCAGTGCTTGGCTATATGGCAAAAATTCAAAATGTGGAT
ATCGATAAAGTTGGATTAGAAGGTCCAGGATTAGTTTTTATTGTATATCCAGAGGCAATT
AGTTTAATGGGTGGCAGCACTTTTTTCTCAATTATTTTCTTCCTCATGTTGATTACACTC
GGTCTTGACTCAACATTTGGTGGTCTTGAGGCGATGATCACGGCACTGTGCGATGAATTT
CCTAACTTTATTGGAAAGCGTCGAAAGTTATTTGTCCTAGTTTTGCTTGCATTTATCTAC
ATTTGTGCATTGCCAACAATGACATACGGTGGTGTTTATTTGGTCAATTTTTTGAATGTC
TATGGCCCAGGTCTGGCAATTTTGTTTGTTGTATTTGTTGAATCGGCTGGCGTTTTCTGG
TTTTATGGAGTTGATAAGTTTAGTGATGACATTGAACAAATGCTTGGACAAAAACCTTCA
TTGTATTGGCGCATTTGTTGGCGTTATATTTCACCAACATTTCTGTTTGTAATTTTGATA
TTTTCCATACTCAATAATGAAGATATGCTTGGAGAAGAGTACTATTATCCTGAATGGGCT
ATTCCTTTAGGATGGCTTTTAACGCTTTCTTCTGTGATCTGTATTCCCCTTTATATGATT
TACAAATTTGATATAAGTCGAGGCAGTTTCAAGAGGAAATTAAGAACGATGTTTAAGCCA
GAGCCTTTAGTGCCCCTGTCTGGTCAAATAAGCACAATGATAAGTACAGTTTGA
>g5704.t1 Gene=g5704 Length=637
MTNENSLDAAESTTNLTSPAKGKIQQINHSEKKGNGEDLAADGYDTWNDERKEEEKESNP
LNPNGSSNAKDKDREERALIVSLTQGRPRETWNQKVEFLLAVIGFAVDLGNVWRFPYICY
QNGGGAFLIPYVIMLLLGGLPLFYMELALGQFHRCGCLSIWNRICPALKGVGMAICIIDI
YMGMYYNTIIGWAVYYFFASFTSELPWEKCGKPWNTEACLSVDIPTNLTNTTTPAREYFE
RNVLEQYKSNGLEYMGPVKPSLALCVFGVFVLVYFSLWKGVKSTGKAVWITALAPYFVLV
VLLIRGVTLDGAGEGIRYYLTPEWEKLKNTKVWIDAASQIFFSLGPGFGTLLALSSYNKF
NNNCYRDALLTSSINCLTSFLAGFVIFSVLGYMAKIQNVDIDKVGLEGPGLVFIVYPEAI
SLMGGSTFFSIIFFLMLITLGLDSTFGGLEAMITALCDEFPNFIGKRRKLFVLVLLAFIY
ICALPTMTYGGVYLVNFLNVYGPGLAILFVVFVESAGVFWFYGVDKFSDDIEQMLGQKPS
LYWRICWRYISPTFLFVILIFSILNNEDMLGEEYYYPEWAIPLGWLLTLSSVICIPLYMI
YKFDISRGSFKRKLRTMFKPEPLVPLSGQISTMISTV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g5704.t1 | CDD | cd11497 | SLC6sbd_SERT-like | 89 | 621 | 0.0 |
| 53 | g5704.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 25 | - |
| 55 | g5704.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 73 | - |
| 54 | g5704.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 26 | 59 | - |
| 2 | g5704.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 56 | 608 | 1.3E-247 |
| 3 | g5704.t1 | PANTHER | PTHR11616:SF279 | SODIUM-DEPENDENT SEROTONIN TRANSPORTER | 56 | 608 | 1.3E-247 |
| 10 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 97 | 118 | 8.0E-75 |
| 8 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 126 | 145 | 8.0E-75 |
| 4 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 170 | 196 | 8.0E-75 |
| 5 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 287 | 304 | 8.0E-75 |
| 6 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 369 | 389 | 8.0E-75 |
| 11 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 423 | 442 | 8.0E-75 |
| 9 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 504 | 524 | 8.0E-75 |
| 7 | g5704.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 544 | 564 | 8.0E-75 |
| 1 | g5704.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 89 | 603 | 1.5E-214 |
| 15 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 95 | - |
| 26 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 115 | - |
| 24 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 116 | 126 | - |
| 30 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 127 | 149 | - |
| 14 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 150 | 169 | - |
| 34 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 198 | - |
| 20 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 199 | 257 | - |
| 27 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 275 | - |
| 19 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 276 | 286 | - |
| 35 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 307 | - |
| 22 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 308 | 335 | - |
| 29 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 357 | - |
| 17 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 358 | 368 | - |
| 28 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 369 | 394 | - |
| 23 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 395 | 413 | - |
| 31 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 414 | 442 | - |
| 16 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 443 | 469 | - |
| 33 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 470 | 494 | - |
| 21 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 495 | 499 | - |
| 37 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 500 | 524 | - |
| 13 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 525 | 544 | - |
| 32 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 545 | 564 | - |
| 25 | g5704.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 565 | 578 | - |
| 36 | g5704.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 601 | - |
| 18 | g5704.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 602 | 637 | - |
| 52 | g5704.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 113 | 127 | - |
| 51 | g5704.t1 | ProSitePatterns | PS00754 | Sodium:neurotransmitter symporter family signature 2. | 196 | 216 | - |
| 56 | g5704.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 88 | 608 | 105.189 |
| 12 | g5704.t1 | SUPERFAMILY | SSF161070 | SNF-like | 89 | 603 | 2.48E-178 |
| 45 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 118 | - |
| 47 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 128 | 150 | - |
| 46 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 171 | 193 | - |
| 50 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 278 | - |
| 42 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 309 | - |
| 40 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 358 | - |
| 43 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 393 | - |
| 41 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 420 | 442 | - |
| 49 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 470 | 492 | - |
| 39 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 502 | 524 | - |
| 44 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 545 | 564 | - |
| 48 | g5704.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 579 | 601 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5704/g5704.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5704.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K05037 (solute carrier family 6 (neurotransmitter transporter, serotonin) member 4)
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.
