General information for g2678.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-binding cassette sub-family G member 4.
Parent gene
- The parent gene g2678 is located on chr_3: 19688801..19693771 (+ 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 | g2678 | g2678.t1 | isoform | g2678.t1 | 19687556 | 19689516 |
| chr_3 | g2678 | g2678.t1 | exon | g2678.t1.exon1 | 19687556 | 19688735 |
| chr_3 | g2678 | g2678.t1 | cds | g2678.t1.CDS1 | 19687556 | 19688735 |
| chr_3 | g2678 | g2678.t1 | exon | g2678.t1.exon2 | 19688800 | 19689056 |
| chr_3 | g2678 | g2678.t1 | cds | g2678.t1.CDS2 | 19688800 | 19689056 |
| chr_3 | g2678 | g2678.t1 | exon | g2678.t1.exon3 | 19689122 | 19689385 |
| chr_3 | g2678 | g2678.t1 | cds | g2678.t1.CDS3 | 19689122 | 19689385 |
| chr_3 | g2678 | g2678.t1 | exon | g2678.t1.exon4 | 19689457 | 19689516 |
| chr_3 | g2678 | g2678.t1 | cds | g2678.t1.CDS4 | 19689457 | 19689516 |
| chr_3 | g2678 | g2678.t1 | TSS | g2678.t1 | NA | NA |
| chr_3 | g2678 | g2678.t1 | TTS | g2678.t1 | NA | NA |
Sequences
>g2678.t1 Gene=g2678 Length=1761
ATGGATAACTCTGTAATTAATCGTGAAAATTTTAAATTTGCATTTAAAAATGTGACATAT
AATATTGGTGTTGAAAACAAATTTTTTAGAAGAAAAGCACGAACCATTTTAAATCAAATC
TCAGGAGAATTTCGTGCAAATGAAATATCAGCTATAATTGGATTGAGTGGTAGCGGTAAA
AGTACATTATTGGATTGTCTCTCTGGATTTCGTAAAAATTATACTAATGGATCATTCCTA
ATAAATGATAATGAGATATCTGTTGAAACTATCAAACGATTAAGTTCATATTTCATGCAA
GAACAAACACTTCATCCATTTCTCACTGTGACAGAAATTTTAATATTTTCATTAAGCATG
AAAGGAGGTGACAATTTAAAAGAAAATGAAAAAAATTTAAGAATTGAACAAATCCTTGAA
AAATTAAGCATTACAAATAGAAATAATACATTGATAAAAGATTTGAGTGGTGGTGAAAAA
AAGAGACTTCAAATCGCAATTGAGCTTGTTAGGGACCCAAAAATTTTATTTCTCGACGAG
CCAACTACAAATCTCGACAGTTTTTCTACAGTACAATGTATAAATTTTTTAAAGTCTCTT
ACGAGAGAGCAAAAAACAGTAATTTGTACCATTCATCAACCATCTGCATCAATTTTTAAG
ATGTTTGATCACATTTATGCCATTTCTAATGGATTTTGTATTTATCAAGGTTCAAGTAAA
AACCTCATTTCATTCTTAAAAGAACTTGGATTAACTTGTCCATTACACTATAATCCAGCT
GACTTTCTCCTTGAAATAGCAAACAATGATTACGGAAATTATAACAAATTACTAATAGAT
AAGATTGAAAATGGAAAAAGAAACTACGAAAATTATGATGAATCTAAATTCGACACAAAT
TCAATTGAAGTCTTCACAAAAGAAAAGAATTATAAAGAAAATTCAGTATCATATTTCTAT
CAAGTTCATCATCTCATGTTAAGAACTTTTCTTTCTACAACACGTGATCGAACGTTATTT
TTTATGCGTTTTGGTCTACATCTTATCATTGGAATTGCATTTGGTTTTATTTATAAGGAT
ATTGGAAGAAAAGGATCAATTGCTTTAGATAATTATCGATTTGCTATTATATCAATTTGT
TTTCTTCTTTACACTTCATATCATTCACTTTATGCAAAATTTCCATTAGAATTTCCAATA
ATAAAAAGAGAGCATTTTAATGGTCTTTATGGAGCAAAAGCTTATTATACAGCAATGATT
TTGTTTGATGCGCCAATTATTCTGATTTGTTGCATAATCTACACTTCAATTACATTTTTC
TTGACTGATCAACCACTCGAACTTTATCGATATTTGATGTTTCTGATGATTTGTCTTGTG
ATGTCTTATGCTGCACAATCTCTTGGTATCATGTTTACCTCACTCATGAATATACAGATG
ACTACAACTTTCGGTACGATTATTATGATGCCGTTCTTTCTTTTCTCGTCGTTCGTGATC
TTTTCCAAGGACACGCATCCATTTTTAATATATTTATTTGACGCAAATTTCATGAATATG
GCCTTCAAAGGATCCGTCAATTCAATAATTGGCCTAAATCGAACAAAATTTGAATGTGAT
GAATTTTATTGTCACTACAGTGATCCTAAAAAAATTCTTCGTGATTTTGAAATGAATGTT
GATATGACACATGCTGTCTTGACACTTATGATCACATATGACCTTGAAATGATTTTTGTA
CTTAAAGAAGAAGAAATATAA
>g2678.t1 Gene=g2678 Length=586
MDNSVINRENFKFAFKNVTYNIGVENKFFRRKARTILNQISGEFRANEISAIIGLSGSGK
STLLDCLSGFRKNYTNGSFLINDNEISVETIKRLSSYFMQEQTLHPFLTVTEILIFSLSM
KGGDNLKENEKNLRIEQILEKLSITNRNNTLIKDLSGGEKKRLQIAIELVRDPKILFLDE
PTTNLDSFSTVQCINFLKSLTREQKTVICTIHQPSASIFKMFDHIYAISNGFCIYQGSSK
NLISFLKELGLTCPLHYNPADFLLEIANNDYGNYNKLLIDKIENGKRNYENYDESKFDTN
SIEVFTKEKNYKENSVSYFYQVHHLMLRTFLSTTRDRTLFFMRFGLHLIIGIAFGFIYKD
IGRKGSIALDNYRFAIISICFLLYTSYHSLYAKFPLEFPIIKREHFNGLYGAKAYYTAMI
LFDAPIILICCIIYTSITFFLTDQPLELYRYLMFLMICLVMSYAAQSLGIMFTSLMNIQM
TTTFGTIIMMPFFLFSSFVIFSKDTHPFLIYLFDANFMNMAFKGSVNSIIGLNRTKFECD
EFYCHYSDPKKILRDFEMNVDMTHAVLTLMITYDLEMIFVLKEEEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2678.t1 | Gene3D | G3DSA:3.40.50.300 | - | 22 | 249 | 4.0E-54 |
| 4 | g2678.t1 | PANTHER | PTHR48041:SF78 | ABC TRANSPORTER EXPRESSED IN TRACHEA, ISOFORM A-RELATED | 9 | 569 | 1.6E-165 |
| 5 | g2678.t1 | PANTHER | PTHR48041 | ABC TRANSPORTER G FAMILY MEMBER 28 | 9 | 569 | 1.6E-165 |
| 3 | g2678.t1 | Pfam | PF00005 | ABC transporter | 37 | 182 | 5.0E-27 |
| 1 | g2678.t1 | Pfam | PF19055 | ABC-2 type transporter | 212 | 267 | 2.0E-7 |
| 2 | g2678.t1 | Pfam | PF01061 | ABC-2 type transporter | 320 | 527 | 4.7E-30 |
| 13 | g2678.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 339 | - |
| 18 | g2678.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 359 | - |
| 10 | g2678.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 360 | 370 | - |
| 17 | g2678.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 394 | - |
| 12 | g2678.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 395 | 413 | - |
| 16 | g2678.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 414 | 441 | - |
| 9 | g2678.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 442 | 447 | - |
| 15 | g2678.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 448 | 472 | - |
| 11 | g2678.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 473 | 477 | - |
| 14 | g2678.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 478 | 501 | - |
| 8 | g2678.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 502 | 586 | - |
| 24 | g2678.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 155 | 169 | - |
| 26 | g2678.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 22 | 255 | 18.874 |
| 25 | g2678.t1 | SMART | SM00382 | AAA_5 | 46 | 232 | 1.1E-12 |
| 6 | g2678.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 13 | 266 | 7.42E-50 |
| 22 | g2678.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 339 | 358 | - |
| 21 | g2678.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 390 | - |
| 19 | g2678.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 419 | 441 | - |
| 23 | g2678.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 448 | 470 | - |
| 20 | g2678.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 480 | 502 | - |
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:0042626 | ATPase-coupled transmembrane transporter activity | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
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.
