General information for g5678.t3
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 g5678 is located on chr_2: 11228091..11229016 (- 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 | g5678 | g5678.t3 | TTS | g5678.t3 | 11223451 | 11223451 |
| chr_2 | g5678 | g5678.t3 | isoform | g5678.t3 | 11223617 | 11224923 |
| chr_2 | g5678 | g5678.t3 | exon | g5678.t3.exon1 | 11223617 | 11223946 |
| chr_2 | g5678 | g5678.t3 | cds | g5678.t3.CDS1 | 11223617 | 11223946 |
| chr_2 | g5678 | g5678.t3 | exon | g5678.t3.exon2 | 11224005 | 11224160 |
| chr_2 | g5678 | g5678.t3 | cds | g5678.t3.CDS2 | 11224005 | 11224160 |
| chr_2 | g5678 | g5678.t3 | exon | g5678.t3.exon3 | 11224214 | 11224923 |
| chr_2 | g5678 | g5678.t3 | cds | g5678.t3.CDS3 | 11224214 | 11224777 |
| chr_2 | g5678 | g5678.t3 | TSS | g5678.t3 | NA | NA |
Sequences
>g5678.t3 Gene=g5678 Length=1196
CAATCTTTACGTTTGATAATGATACAGGAATTGGTAAAAATATAACAATCAATATTATAT
CTGGTATTTTATTTTTGAGCATTTGTTTGTTGAAAGATCATCTCATTTTTGAATCTATAT
ACTACAAATTCTTTAACCGTCCAAGAATGCTTCCATTGCTGAATCAGAATATAGACAATG
ATGTTGATGAAGAAATACAAAAGGTCAAAGAGATGTCATATGATGAAATTAGGCAAAGTA
ATCTTGTGTTACAAGGCTTAACAAAATTTTATGGAAACTTTCTAGCTGTGAATCAATTAT
ATCTTGATATAAAACGTAAAGAATGTTTCGGCTTGCTTGGAATCAATGGAGCAGGTAAAA
CCTCAACATTCAAAATGATGACTGGAGACGAACTTATTTCGGCTGGTGATGCATATGTTT
CTGGATTTAGTATGAAAAATAATTTAAGTAAAGTTCATCAGCATATAAGTTATTGCCCAC
AATTTGACGCTGTTATCAGTGAACTTACCGGACAAGAAACGTTGAAAATATTCTCACTGA
TACGTGGTATACCTAAACATGAAATAAATGAAAATCTCTATAGAATGGCAACTGAACTTG
GATTTCAACAACATTTGAAGAAGCAGGTCAAAGCATTTAGCGGAGGCAACAAAAGAAAAC
TCTCTACTTGCTTGGCTTTATTAGGAAATCCACAGTTAATATTTTTAGATGAACCAACCA
CAGGAATTGATGTTGAAGCAAAGCGCAAATTATGGAACGTAATTAACCAAACTCGAAATG
CAGGCCGCTCAATTGTTATAACTTCTCATAGCATTGATGAATGTGAAGCTTTATGTACCA
AAATCGGAATTATGGTCAATGGTCAGTTTAAGTGTCTTGGATCTGTTCAACATTTGAAGA
ACAAATATTCAAAAGGATTTGTTCTAACTATTAAAATGCTACGAGATGATCCTGAACTTA
AAATTCAAATTGAGAAGCGTGTGGCAGAATCATTTTCATCGGCAGAATTAAAGGAAAAGT
ATTTGTGTCTTTTAACTTTTCATATAACTAATACAGACTTGAAATGGTCAGAAGTTTTTG
CAAACTGCTCTCGAATGAAGGCGGATCTCGATATTAGTGATTATTCGTTGACACAAATGT
CATTGGAACAAGTCTTTATATTATTTTCTAAGAGTGGAATCTACCAAAATCAATAA
>g5678.t3 Gene=g5678 Length=349
MLPLLNQNIDNDVDEEIQKVKEMSYDEIRQSNLVLQGLTKFYGNFLAVNQLYLDIKRKEC
FGLLGINGAGKTSTFKMMTGDELISAGDAYVSGFSMKNNLSKVHQHISYCPQFDAVISEL
TGQETLKIFSLIRGIPKHEINENLYRMATELGFQQHLKKQVKAFSGGNKRKLSTCLALLG
NPQLIFLDEPTTGIDVEAKRKLWNVINQTRNAGRSIVITSHSIDECEALCTKIGIMVNGQ
FKCLGSVQHLKNKYSKGFVLTIKMLRDDPELKIQIEKRVAESFSSAELKEKYLCLLTFHI
TNTDLKWSEVFANCSRMKADLDISDYSLTQMSLEQVFILFSKSGIYQNQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5678.t3 | CDD | cd03263 | ABC_subfamily_A | 33 | 251 | 0.000 |
| 5 | g5678.t3 | Gene3D | G3DSA:3.40.50.300 | - | 20 | 264 | 0.000 |
| 2 | g5678.t3 | PANTHER | PTHR19229:SF49 | ATP-BINDING CASSETTE SUB-FAMILY A MEMBER 7 | 8 | 344 | 0.000 |
| 3 | g5678.t3 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 8 | 344 | 0.000 |
| 1 | g5678.t3 | Pfam | PF00005 | ABC transporter | 49 | 191 | 0.000 |
| 6 | g5678.t3 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 33 | 263 | 17.921 |
| 4 | g5678.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 33 | 254 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5678/g5678.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5678.t3.fa.iupred3.txt does not exist
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 transcript has been annotated with K25182 (drug efflux transport system ATP-binding protein)
Pathway
This gene does not belong to any 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.
