General information for g1835.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-binding cassette sub-family G member 1.
Parent gene
- The parent gene g1835 is located on chr_3: 13234918..13236805 (+ 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_3 | g1835 | g1835.t1 | TSS | g1835.t1 | 13234875 | 13234875 |
| chr_3 | g1835 | g1835.t1 | isoform | g1835.t1 | 13234918 | 13236805 |
| chr_3 | g1835 | g1835.t1 | exon | g1835.t1.exon1 | 13234918 | 13234987 |
| chr_3 | g1835 | g1835.t1 | cds | g1835.t1.CDS1 | 13234918 | 13234987 |
| chr_3 | g1835 | g1835.t1 | exon | g1835.t1.exon2 | 13235050 | 13236392 |
| chr_3 | g1835 | g1835.t1 | cds | g1835.t1.CDS2 | 13235050 | 13236392 |
| chr_3 | g1835 | g1835.t1 | exon | g1835.t1.exon3 | 13236458 | 13236805 |
| chr_3 | g1835 | g1835.t1 | cds | g1835.t1.CDS3 | 13236458 | 13236805 |
| chr_3 | g1835 | g1835.t1 | TTS | g1835.t1 | 13236972 | 13236972 |
Sequences
>g1835.t1 Gene=g1835 Length=1761
ATGAATAGTTTGATTAACATAAAATTTGATGAATTATCGTATAGTGTTGAGGAAATTTTT
TTTAAGGACCGTAAAAAAGAAATTTTAAAAAGAATCAGTGGAAATTTTTATGGATCAGAA
CTTACAGCAATATTAGGTCCAAGCGGTAGTGGCAAGAGTACTTTAATGAATTTACTATTC
GGTTTTGAACAAAAATATGTATGTGGAACAATTTCAATGAATGGATGTTCAATCAATAAA
TTTCGTAGAAATATTGTTTACATCACACAAGAAAATAATTTACAACCATTGCTTACTGTT
GGCGAATCAATGAATTTTGCTATAAAATTTAAAATCGGCAATCAAATGAATTCATTCAAA
AAATGGATTAAAATTGCAGAAATTTTAAAATCTTTTGGTCTATTTGAAGTTGAAAGTGAA
TATGTGAAAAATTTAAGTGGCGGTCAACAAAAAAGACTATCAATTGCATTAGAAATTGTA
GATGATCCAAAAGTAATTTTTCTTGATGAGCCTACTACAGGACTTGACAGTGTATCATCA
ACTATATGCATAAATTTAATGAGACAGCTTGCACAAGAAGGCAAAACTGTTGTATGTACA
ATTCATCAACCAACTACAAATCAACTTAAAAGTTTCTCACATCTTTATATTCTCGCAAAT
GGAGAGTGTGCATATCAAGGAAATGGGAAAAATCTTGTTCCATTTTTAAGCGAACTCAAT
CTCATATGTCCAAGCACTTTCAATCCCGCAGATTTTTTGCTAGAAACAGTTACTGGAATT
TATGGACAAGAGCACATTAGTAAATTAATAGAAAAGATCGATAATGGTAAAAATGAAAAT
TTTCGAACAAAAAAATCGATTGAAATTGACGACAGTGATAGCCTTGAAGCAGTAGCAATT
TACAACAGTTCGACCTACTCTCCTTCGTTTTTATCGAAGTTTAATGATTTACTGGTTCGT
AATTTTATTATTATGTTTCGAGATAAAAGTTTATTCAAAATTCGCATGTTCATGCACATT
ATGACAGGATTATTGCTTGGATTACTTTACTATGATATTGGTAATGATGCACAAAATATT
ATAGACAATTTTCGACTTATTTTTGTGGCCCTTAGCTTCTTAACCTATACTGCCTATTAT
AGCATAATGGTGGCTTTTCCATTAAATTTTTCAAGTGTAAGACGAGAAACATTCAATCGA
TGGTACACACCATCAATTTTTTACATCAATTTAATCTTAACTGACTTGCCTACTCTTATA
TTAGGAATATTTGCATTTATCTTGCCTATGTATTATTTAACATCACAACCATTAGAATTT
TTACGTTTTGCAACTTTTTCATTGATTATGACTTTAAATAGCATTTGTTCACAAGCATTT
GGATTGATTGCTGGCTCATTTGCAGGACTTAAGCAAACTTTAATACTTGCACCTGTATTT
ATGATTTTTCACGGTGCATTTTCTGGTTTTTATATTTTAAAAAAAGATGCTCATTCAATC
TGGCATCCATTCTTTGAGATATCATATTTAAAGTATGCAGCTTATGGATCAGAAATGAGT
ATATTAGGTTTTAATAGAACCAAAATGGAATGCAATGCAATTTATTGTCACTACAGTTCA
CCAGGAAAATTTCTGCAGACACTCGAGTATGCTTCAGATATGAATGATTTTATCACATGT
GTTTTCATGTTAGTGGTAAATTCAATTATCAATTTTATATTCGCATATTTTCTTATTAAA
CGTCGTTTAAAGACAAAATAA
>g1835.t1 Gene=g1835 Length=586
MNSLINIKFDELSYSVEEIFFKDRKKEILKRISGNFYGSELTAILGPSGSGKSTLMNLLF
GFEQKYVCGTISMNGCSINKFRRNIVYITQENNLQPLLTVGESMNFAIKFKIGNQMNSFK
KWIKIAEILKSFGLFEVESEYVKNLSGGQQKRLSIALEIVDDPKVIFLDEPTTGLDSVSS
TICINLMRQLAQEGKTVVCTIHQPTTNQLKSFSHLYILANGECAYQGNGKNLVPFLSELN
LICPSTFNPADFLLETVTGIYGQEHISKLIEKIDNGKNENFRTKKSIEIDDSDSLEAVAI
YNSSTYSPSFLSKFNDLLVRNFIIMFRDKSLFKIRMFMHIMTGLLLGLLYYDIGNDAQNI
IDNFRLIFVALSFLTYTAYYSIMVAFPLNFSSVRRETFNRWYTPSIFYINLILTDLPTLI
LGIFAFILPMYYLTSQPLEFLRFATFSLIMTLNSICSQAFGLIAGSFAGLKQTLILAPVF
MIFHGAFSGFYILKKDAHSIWHPFFEISYLKYAAYGSEMSILGFNRTKMECNAIYCHYSS
PGKFLQTLEYASDMNDFITCVFMLVVNSIINFIFAYFLIKRRLKTK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1835.t1 | Gene3D | G3DSA:3.40.50.300 | - | 6 | 235 | 1.2E-52 |
| 3 | g1835.t1 | PANTHER | PTHR48041:SF78 | ABC TRANSPORTER EXPRESSED IN TRACHEA, ISOFORM A-RELATED | 4 | 580 | 5.6E-172 |
| 4 | g1835.t1 | PANTHER | PTHR48041 | ABC TRANSPORTER G FAMILY MEMBER 28 | 4 | 580 | 5.6E-172 |
| 2 | g1835.t1 | Pfam | PF00005 | ABC transporter | 29 | 172 | 4.1E-28 |
| 1 | g1835.t1 | Pfam | PF01061 | ABC-2 type transporter | 317 | 516 | 1.4E-24 |
| 8 | g1835.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 333 | - |
| 14 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 353 | - |
| 11 | g1835.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 354 | 364 | - |
| 15 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 386 | - |
| 7 | g1835.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 387 | 406 | - |
| 16 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 407 | 428 | - |
| 13 | g1835.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 429 | 439 | - |
| 18 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 440 | 462 | - |
| 10 | g1835.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 463 | 473 | - |
| 17 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 493 | - |
| 12 | g1835.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 494 | 556 | - |
| 19 | g1835.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 557 | 579 | - |
| 9 | g1835.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 580 | 586 | - |
| 26 | g1835.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 145 | 159 | - |
| 28 | g1835.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 7 | 245 | 19.141 |
| 27 | g1835.t1 | SMART | SM00382 | AAA_5 | 38 | 221 | 7.5E-12 |
| 5 | g1835.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 16 | 237 | 1.33E-46 |
| 25 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 353 | - |
| 24 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 368 | 390 | - |
| 21 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 428 | - |
| 20 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 465 | - |
| 22 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 493 | - |
| 23 | g1835.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 557 | 579 | - |
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:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05685 (macrolide transport system ATP-binding/permease protein [EC:7.6.2.-])
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.
