General information for g1987.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative ABC transporter G family member 20.
Parent gene
- The parent gene g1987 is located on chr_3: 14228767..14229943 (+ 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 | g1987 | g1987.t13 | isoform | g1987.t13 | 14227497 | 14228767 |
| chr_3 | g1987 | g1987.t13 | exon | g1987.t13.exon1 | 14227497 | 14227695 |
| chr_3 | g1987 | g1987.t13 | cds | g1987.t13.CDS1 | 14227535 | 14227695 |
| chr_3 | g1987 | g1987.t13 | exon | g1987.t13.exon2 | 14227762 | 14228133 |
| chr_3 | g1987 | g1987.t13 | cds | g1987.t13.CDS2 | 14227762 | 14228133 |
| chr_3 | g1987 | g1987.t13 | exon | g1987.t13.exon3 | 14228203 | 14228589 |
| chr_3 | g1987 | g1987.t13 | cds | g1987.t13.CDS3 | 14228203 | 14228589 |
| chr_3 | g1987 | g1987.t13 | exon | g1987.t13.exon4 | 14228646 | 14228767 |
| chr_3 | g1987 | g1987.t13 | cds | g1987.t13.CDS4 | 14228646 | 14228766 |
| chr_3 | g1987 | g1987.t13 | TSS | g1987.t13 | NA | NA |
| chr_3 | g1987 | g1987.t13 | TTS | g1987.t13 | NA | NA |
Sequences
>g1987.t13 Gene=g1987 Length=1080
AATTAATTCATAAAATCAGTCTTGAATTAGCGCTCAGTATGGATAGCAGCACAGAGCTTC
AGCTAGAAAAAATTAATAACGGCGTCGTGTCGTGTGATTATGCAGTAAAAATTCGGAATG
CATACAAGTGTTTTCAACAAAGGAATGAGAAGGTCGAAATTCTTAAAAGATTAAATATGT
CGATAAAAAAGAAATCAATATATGCACTGATGGGTTGTAGTGGTGTAGGAAAAACAACTT
TATTACGTTCTATAATTGCAATTGATACACTACAAAGTGGGAAAATTGAAATTTTTGGTG
AACCAGTAGTTCAAAATGATCCTAGAATCGGTTTTATGCCTCAGGAAATTTCACTCATCG
AAAATTTTACAGTGAAAGAAATGGTCGATTTTTTCAGTGTATTATACAAATTGAGAACTG
AGAAAATCAATGCACGATTTAAATTTTTAAGTGAATTACTTGAACTTCCCGATGATAATA
AATTTATTAAAGAATGCAGTCTCGGTGAAAAAAGGCGAATTTCGTTTGCATGTGCTTTAG
TTCATGAGCCAAAAATTTTAATTTTAGATGAACCAACAGTTGGTATTGACGCAGTGCTAC
GTAAAAAGATTTGGGATTTTCTAATAGAACTTGTAGCTACTTCTGACACTACTGTAATAA
TTTCAACACATTATATTCAAGAATCAATGAATTCCACGTGTGTAGGATTAATGAGAAATG
GAAAAATTTTAATTGAAGATAAACCACAAGACATTATTCAAAGATATAACACAAAGAATT
TAGAGGAAGCATTTTTGATACTGAGCGATGAACAAGATAAGAGTCTTAGTGTTTCAGAAA
CAAATGAAGAAGAATTTGATTTTCTTTATCATGTGCCGAAGCAATCGTTCAATTTTTCAA
TGAAACGGTTAATGGCGCTTTTAACAAAAAATTTTATTCATCAGAAAAGAAGCAAGACAA
TGTTTATGTTTCTTTGTGTTTTTCCGCTAATCGTACTCATGAGTATTGCTACATTTGGAA
GAGATCCACAGGGATTAAAGATAGGCATAGTTGATGATGAAGTTGATAACCTTGAACAAT
>g1987.t13 Gene=g1987 Length=347
MDSSTELQLEKINNGVVSCDYAVKIRNAYKCFQQRNEKVEILKRLNMSIKKKSIYALMGC
SGVGKTTLLRSIIAIDTLQSGKIEIFGEPVVQNDPRIGFMPQEISLIENFTVKEMVDFFS
VLYKLRTEKINARFKFLSELLELPDDNKFIKECSLGEKRRISFACALVHEPKILILDEPT
VGIDAVLRKKIWDFLIELVATSDTTVIISTHYIQESMNSTCVGLMRNGKILIEDKPQDII
QRYNTKNLEEAFLILSDEQDKSLSVSETNEEEFDFLYHVPKQSFNFSMKRLMALLTKNFI
HQKRSKTMFMFLCVFPLIVLMSIATFGRDPQGLKIGIVDDEVDNLEQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1987.t13 | CDD | cd03230 | ABC_DR_subfamily_A | 23 | 230 | 1.51157E-51 |
| 7 | g1987.t13 | Gene3D | G3DSA:3.40.50.300 | - | 19 | 279 | 1.7E-52 |
| 3 | g1987.t13 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 22 | 267 | 9.0E-96 |
| 5 | g1987.t13 | PANTHER | PTHR43038:SF2 | RH61964P | 22 | 267 | 9.0E-96 |
| 2 | g1987.t13 | PANTHER | PTHR43038 | ATP-BINDING CASSETTE, SUB-FAMILY H, MEMBER 1 | 281 | 345 | 9.0E-96 |
| 4 | g1987.t13 | PANTHER | PTHR43038:SF2 | RH61964P | 281 | 345 | 9.0E-96 |
| 1 | g1987.t13 | Pfam | PF00005 | ABC transporter | 42 | 180 | 1.1E-23 |
| 9 | g1987.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 307 | - |
| 10 | g1987.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 308 | 327 | - |
| 8 | g1987.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 328 | 347 | - |
| 13 | g1987.t13 | ProSitePatterns | PS00211 | ABC transporters family signature. | 153 | 167 | - |
| 15 | g1987.t13 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 23 | 252 | 18.181 |
| 14 | g1987.t13 | SMART | SM00382 | AAA_5 | 51 | 236 | 7.8E-7 |
| 6 | g1987.t13 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 22 | 244 | 2.77E-48 |
| 12 | g1987.t13 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 307 | 326 | - |
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 K15555 (sulfonate transport 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