General information for g4196.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ABC transporter G family member 23.
Parent gene
- The parent gene g4196 is located on chr_2: 15847..24471 (+ 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 | g4196 | g4196.t1 | isoform | g4196.t1 | 15847 | 24471 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon1 | 15847 | 15956 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS1 | 15847 | 15956 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon2 | 18250 | 19035 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS2 | 18250 | 19035 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon3 | 19116 | 19664 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS3 | 19116 | 19664 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon4 | 19718 | 20080 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS4 | 19718 | 20080 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon5 | 20140 | 20216 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS5 | 20140 | 20216 |
| chr_2 | g4196 | g4196.t1 | exon | g4196.t1.exon6 | 24218 | 24471 |
| chr_2 | g4196 | g4196.t1 | cds | g4196.t1.CDS6 | 24218 | 24219 |
| chr_2 | g4196 | g4196.t1 | TSS | g4196.t1 | NA | NA |
| chr_2 | g4196 | g4196.t1 | TTS | g4196.t1 | NA | NA |
Sequences
>g4196.t1 Gene=g4196 Length=2139
ATGAAGTGTATAGAAGTAAAAGATGTGAGCAAATTTTATCATGAAAAAAGACACAATAAA
AATTTAAAAATTCTAAATGGAATAAATGTGACAGTTCCTACTGGCACAATTTATACTCTT
GTTGGACCTTCAAGTTGCGGTAAAACGACACTTTTGACCTGCATTTTAGGTTTGCAAAAG
TTTCAAAACGGTGAAATAAAAATTTTCAATAGAAAAATTGAGTTTAATAAAACTTCAAAA
TTTTCGCATTTAATTGGCTATATGCCTCAACAAAAATCTTTGCCTTCTAATTTGACAATC
TTCGAAACATTGCAGTATTTTGGAAATATTCACTTAATGAATCAAGAAACATTCTATGAA
CGTTTTGAAATGATTTCAAAATTATTTGAATTGCCAAGAAAAGACAAGTTAATAAAAGAA
TTGTCGGGTGGTGAACAAAGACGAATTTCTCTTGCTATCACAATAATTCATAATCCAAAA
CTTCTCATTTTGGACGAGCCAACTGTCGGTGTTGATTTTGAAATTCGTGACAAAATTTGG
AAATTTTTAACTACACAAAGTAAGGAAACAAAATTGACAGTTTTGATAACGACACATTAT
CTCAATGAAACTGAAAAAGCAGATCGATGTGGATTTATGAAAAGAGGAGTTTTAGTAGCT
GAAAATTCGCCAAACAAGATTATACAACATTTTTGTGTTAATAAACTCGACGATGCATTT
ATTGAAATTTATTCTAATGACAAAACCTGTTTTGATGATGCAGATAGTAATAAATTTGAA
ACATTTTCAGAAGAACATGAAGATTTAGGAATTAATAAAGATAAAATAATGATCAGACAT
CAAGTTTTAAAAGGTCTTTTATTGAAAGAATGGCATAGAATAAAAAGGCAAAAAATAGAT
TTTGTAACAATATTCATCATGTCCTCAGCAATTCTTGGTCTAGTTTATATCTTACTTGGC
AGTTTTCCTAATGATCTTAAAGTGGCGGTTGTTTTAAGTGAAAATTTACAAAAATGTACA
ATAAATCTAAATGACAAACTTTCAAAATTTGAATTATGTAACAACAATACAAAACTTTTG
TGTGAATTCTTGAATCAAATGACCGATGTTGACAAAATAATTTATGAAAATTACACAGAA
GCAAATATAGATTTTAAACATGGTACTATTTTTGGATTTATTTCTTTGGGATCAAATTTT
ATATCATCACTAATTGAAAATAACACAAAAAATATTGAAATTCATATTGATTCATCGAAA
ATTTTTTTTAAAGATTTTGTGAATTACAAAATATTTTCAACACTTGAAATTTTTACAAAA
ATATTAAAAGAAAGGTGTGACATCAATACAAATTCAATGTTACCTTATATGCAAGTAACT
GATTTACAAGAAATATCTTTGAATTTTGATCTATCAAAATTTATAACGATCAATATGTTA
GCAATGGCAGCATTTATAACTCCAATGATTTATTCAGGTTTGATCATTTATGAGTGCCGT
AGTGAAGGAATTTGGGAGAGAACCTATTTAAGTGGTGTGAAAGTGATTGAGATTATTACT
GCTTATATCATTCAGTGCATTTTTGTGTCATTACTTGTAACTGTTGAAATTTTTATTTTT
TTAATTTATGTTTTAAATGTTGATGTCTTAAGTCATCAATTTCTCATAATTTTTATACTA
TTTGAACTTGCAACTCTTGGATATTTGTCTGGTTTTCTTACTTCAATTTTCTTCAAAACA
CTTGTTGGAATCTCTGGATTTTGCATGGGAATTATAATGATTCAATTCATGGCTTCTGGA
ATTATGTGGCCATTGGAAACAGCAATGATTTATATTTATCCAATTTCATATAGCAGTCCA
TTAACACTTTCAAGACAATTGTTTTAACAACGTTACAAAGCAAAAATACTACAAAGTGCT
CCTAAGGGTTTATCAGAACATTTGAAACGAGTTGTTCAGTTAGTAAAATCACATTTAAGT
TCTTTTCATATTGATACAGAAAAAGATGTGATTTTATATTCAAATGATGGAGCAGCTTTG
ATGAAAAAATTTGGTTTTCTAATGAACCTTCCATTGCATTTCTCAACCAGCAAAAATTGC
AATAGATTAACTCTCAAAAGACACAAGAGACACGATTGA
>g4196.t1 Gene=g4196 Length=628
MKCIEVKDVSKFYHEKRHNKNLKILNGINVTVPTGTIYTLVGPSSCGKTTLLTCILGLQK
FQNGEIKIFNRKIEFNKTSKFSHLIGYMPQQKSLPSNLTIFETLQYFGNIHLMNQETFYE
RFEMISKLFELPRKDKLIKELSGGEQRRISLAITIIHNPKLLILDEPTVGVDFEIRDKIW
KFLTTQSKETKLTVLITTHYLNETEKADRCGFMKRGVLVAENSPNKIIQHFCVNKLDDAF
IEIYSNDKTCFDDADSNKFETFSEEHEDLGINKDKIMIRHQVLKGLLLKEWHRIKRQKID
FVTIFIMSSAILGLVYILLGSFPNDLKVAVVLSENLQKCTINLNDKLSKFELCNNNTKLL
CEFLNQMTDVDKIIYENYTEANIDFKHGTIFGFISLGSNFISSLIENNTKNIEIHIDSSK
IFFKDFVNYKIFSTLEIFTKILKERCDINTNSMLPYMQVTDLQEISLNFDLSKFITINML
AMAAFITPMIYSGLIIYECRSEGIWERTYLSGVKVIEIITAYIIQCIFVSLLVTVEIFIF
LIYVLNVDVLSHQFLIIFILFELATLGYLSGFLTSIFFKTLVGISGFCMGIIMIQFMASG
IMWPLETAMIYIYPISYSSPLTLSRQLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g4196.t1 | CDD | cd03230 | ABC_DR_subfamily_A | 4 | 218 | 1.23182E-49 |
| 8 | g4196.t1 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 249 | 4.0E-56 |
| 4 | g4196.t1 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 1 | 244 | 3.3E-105 |
| 6 | g4196.t1 | PANTHER | PTHR43038:SF2 | RH61964P | 1 | 244 | 3.3E-105 |
| 3 | g4196.t1 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 250 | 624 | 3.3E-105 |
| 5 | g4196.t1 | PANTHER | PTHR43038:SF2 | RH61964P | 250 | 624 | 3.3E-105 |
| 2 | g4196.t1 | Pfam | PF00005 | ABC transporter | 25 | 168 | 5.1E-29 |
| 1 | g4196.t1 | Pfam | PF12698 | ABC-2 family transporter protein | 303 | 614 | 3.4E-15 |
| 11 | g4196.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 298 | - |
| 19 | g4196.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 299 | 319 | - |
| 12 | g4196.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 320 | 473 | - |
| 16 | g4196.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 497 | - |
| 10 | g4196.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 498 | 517 | - |
| 15 | g4196.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 518 | 544 | - |
| 14 | g4196.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 545 | 549 | - |
| 18 | g4196.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 550 | 569 | - |
| 9 | g4196.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 570 | 580 | - |
| 17 | g4196.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 581 | 603 | - |
| 13 | g4196.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 604 | 628 | - |
| 26 | g4196.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 141 | 155 | - |
| 28 | g4196.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 4 | 240 | 19.701 |
| 27 | g4196.t1 | SMART | SM00382 | AAA_5 | 34 | 224 | 3.6E-7 |
| 7 | g4196.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 4 | 231 | 3.7E-52 |
| 24 | g4196.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 301 | 323 | - |
| 25 | g4196.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 475 | 497 | - |
| 23 | g4196.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 518 | 540 | - |
| 22 | g4196.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 555 | 577 | - |
| 21 | g4196.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 582 | 604 | - |
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:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K06861 (lipopolysaccharide export system ATP-binding 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. There were no conditions that were differentially expressed