General information for g13175.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP-binding cassette sub-family A member 3.
Parent gene
- The parent gene g13175 is located on chr_1: 28334804..28336766 (+ 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_1 | g13175 | g13175.t4 | isoform | g13175.t4 | 28333538 | 28334804 |
| chr_1 | g13175 | g13175.t4 | exon | g13175.t4.exon1 | 28333538 | 28334216 |
| chr_1 | g13175 | g13175.t4 | cds | g13175.t4.CDS1 | 28333611 | 28334216 |
| chr_1 | g13175 | g13175.t4 | exon | g13175.t4.exon2 | 28334283 | 28334328 |
| chr_1 | g13175 | g13175.t4 | cds | g13175.t4.CDS2 | 28334283 | 28334328 |
| chr_1 | g13175 | g13175.t4 | exon | g13175.t4.exon3 | 28334388 | 28334553 |
| chr_1 | g13175 | g13175.t4 | cds | g13175.t4.CDS3 | 28334388 | 28334553 |
| chr_1 | g13175 | g13175.t4 | exon | g13175.t4.exon4 | 28334612 | 28334804 |
| chr_1 | g13175 | g13175.t4 | cds | g13175.t4.CDS4 | 28334612 | 28334804 |
| chr_1 | g13175 | g13175.t4 | TSS | g13175.t4 | NA | NA |
| chr_1 | g13175 | g13175.t4 | TTS | g13175.t4 | NA | NA |
Sequences
>g13175.t4 Gene=g13175 Length=1084
ATTGAAAAACATTCCCGAATCAGAGGAAAATTTCATTGATGCTGATGTATTGGCTGAAAA
AGACAAAATCAGAATGTATACACAATATTTAGTTGCAAAAAATAATTTAGTGATGAAAAA
TTTTACAAAATTTTATGGAAATTTTATGGCAGTCAATCAACTTTGCGTAGGTGTGGATAG
AGCTGAATGCTTTGGACTGTTAGGTGTGAACGGCGCAGGCAAAACATCAGCATTTAAGAT
GTTAGTTGGTGATGAAAGCATTTCAGCTGGTGATGCATGGGTTGATGGTTTCAGCATTCG
AACTCAGTTAAATAAAGTTCATAAACGAATTGGATATTGCCCACAATTTGATGCTCTCAT
TGAAGATCTTACTGGAAGAGAAACATTGAAAATTTTTGCACTTTTGAGGGGAATTTCTCG
TGATAGCATTAATCAAATTGCAGAACAATTGGCAGAAGATTTAAATTTTACAAAGCATCT
TGATAAGAAGACAAAGGAATATAGTGGAGGAAATAAAAGAAAATTGAGCACAGCATTGAC
ATTAATTGGGGATCCATCAGTTATTTATTTAGATGAACCTACAAGTGGGATGGATGTAGG
TGCAAGAAGACAATTGTGGAATATGGTAATTAAAGCAAGAAACTCAGGAAAATCAATCGT
TTTGACTTCGCATAGCATGGAAGAGTGTGAAGTATTATGTAACAGACTTGCTATCATGGT
TAATGGTGAATTCAAATGCTTAGGTTCAGTTCAGCATTTGAAGAATAAATTTTCTAAAGG
ATTTTTCCTCACAATCAAAATTGGAAATAATGATGACGTTCATATGCTGAATCGAAAAAT
AATCGTCGTTAAAGATTTTGTTGCAAATACATTTAGCGGTGCAATACTTAAGGAAGAATT
TATGGATTTACTTTCATATCACATACCAACTGAACAACTAAAATGGTCAAATATTTTTGG
TATAATGGAAGATGCAAAGCAAAAATTAGGCATCTCAGATTACTCTTTGGGTCAAACATC
CCTTGAACAAGTCTTTTTGTATTTCACAAAAACTCAGAGAATTTCAGATAAGAAAGACAA
ATAA
>g13175.t4 Gene=g13175 Length=336
MYTQYLVAKNNLVMKNFTKFYGNFMAVNQLCVGVDRAECFGLLGVNGAGKTSAFKMLVGD
ESISAGDAWVDGFSIRTQLNKVHKRIGYCPQFDALIEDLTGRETLKIFALLRGISRDSIN
QIAEQLAEDLNFTKHLDKKTKEYSGGNKRKLSTALTLIGDPSVIYLDEPTSGMDVGARRQ
LWNMVIKARNSGKSIVLTSHSMEECEVLCNRLAIMVNGEFKCLGSVQHLKNKFSKGFFLT
IKIGNNDDVHMLNRKIIVVKDFVANTFSGAILKEEFMDLLSYHIPTEQLKWSNIFGIMED
AKQKLGISDYSLGQTSLEQVFLYFTKTQRISDKKDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13175.t4 | CDD | cd03263 | ABC_subfamily_A | 12 | 230 | 0.000 |
| 5 | g13175.t4 | Gene3D | G3DSA:3.40.50.300 | - | 3 | 242 | 0.000 |
| 2 | g13175.t4 | PANTHER | PTHR19229:SF49 | ATP-BINDING CASSETTE SUB-FAMILY A MEMBER 7 | 9 | 330 | 0.000 |
| 3 | g13175.t4 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 9 | 330 | 0.000 |
| 1 | g13175.t4 | Pfam | PF00005 | ABC transporter | 28 | 171 | 0.000 |
| 6 | g13175.t4 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 12 | 242 | 18.414 |
| 4 | g13175.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 12 | 233 | 0.000 |
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:0055085 | transmembrane transport | BP |
| GO:0005524 | ATP binding | MF |
| GO:0042626 | ATPase-coupled transmembrane transporter activity | MF |
| GO:0016021 | integral component of membrane | CC |
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.
