General information for g535.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative ATP-binding cassette sub-family A member 3.
Parent gene
- The parent gene g535 is located on chr_3: 3971392..3975754 (+ 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 | g535 | g535.t6 | TSS | g535.t6 | 3970722 | 3970722 |
| chr_3 | g535 | g535.t6 | isoform | g535.t6 | 3970971 | 3974238 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon5 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS5 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon6 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS6 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t6 | exon | g535.t6.exon7 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t6 | cds | g535.t6.CDS7 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t6 | TTS | g535.t6 | NA | NA |
Sequences
>g535.t6 Gene=g535 Length=987
ATGGAGAATTGTGAATATAGCATTATTGGAACGGGTCGTCAAGTAGGAGACTCAGACGTT
AGGATGACATCGAAATGGGCCAAATTTAGACTGTTGATGTGGAAAAATTACCTTCTTCAG
TATCGTCATCCATTTCAAACAATTCTTGAGATTGCTATACCAGTATTATTTTCAGCATTA
CTCGTACTCATTCGTAGCTTAGTATCACCCGACATTTTTTCAGATCCAACGATCTATCCA
CCTTTACCATTAACTGATATCAAACAGACCTTTGGCGCTAGAGGAGAGTTTGCTTTCAAA
GTTCTCTCATTTAACAAGAACATCAATATTTCACAATTTACAAACTTTTCTAATGAAATC
GTCTACTCACCGGATAACATTGAAGTCAATGCATTGATGAAAGAGTTAAATAGTTATGTG
AAACCTTTCCTTAAGGTCACTCCTGTGCCTTCATCAAATGAACTAGCTCCGTACTTAAGA
AAATCAAATGCTTATGTTGGAATTGAATTTCCTGATAACTATAAAAACATAACAGAACTA
CCAGATGATCTCGAATACAGTATACGATATCCAGGAGAATTACGAAGAACAGGAGGAGCT
TTAAATCCATTATTTTTCAACTGGCGAACAGATTTTCTTTTTCCACTTTTTCAACCGGGT
GGCTCGAGAAATTTCAACAACACTCATGACGGATTGCCTAGTGGCTATTATATTGAAGGA
TTTTTATTTGTTCAACAATTTATGTTTAAAGCTTTCTCGACTTTGAAAAATAAAATGGAC
ATTGACCTAAAACAATTACCAAAAATCAATATAAGGAGATTTCCTTATCCACCTTTTGTT
CTTGATATATTACTGCAGGGACTTCAATCACTTGTTTCACTTTTTATCTTGCTAAGTTTT
GTTTATCCTTGCATTAACATCATCAAGTACATCACAACTGAAAAAGAAAAACAACTAAAA
GAAGCTATGAAAATTATGGGATTAGAT
>g535.t6 Gene=g535 Length=329
MENCEYSIIGTGRQVGDSDVRMTSKWAKFRLLMWKNYLLQYRHPFQTILEIAIPVLFSAL
LVLIRSLVSPDIFSDPTIYPPLPLTDIKQTFGARGEFAFKVLSFNKNINISQFTNFSNEI
VYSPDNIEVNALMKELNSYVKPFLKVTPVPSSNELAPYLRKSNAYVGIEFPDNYKNITEL
PDDLEYSIRYPGELRRTGGALNPLFFNWRTDFLFPLFQPGGSRNFNNTHDGLPSGYYIEG
FLFVQQFMFKAFSTLKNKMDIDLKQLPKINIRRFPYPPFVLDILLQGLQSLVSLFILLSF
VYPCINIIKYITTEKEKQLKEAMKIMGLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g535.t6 | PANTHER | PTHR19229:SF139 | ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 14 | 27 | 328 | 6.3E-33 |
| 3 | g535.t6 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 27 | 328 | 6.3E-33 |
| 1 | g535.t6 | Pfam | PF12698 | ABC-2 family transporter protein | 47 | 328 | 1.8E-8 |
| 6 | g535.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 44 | - |
| 9 | g535.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 5 | g535.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 278 | - |
| 8 | g535.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 279 | 302 | - |
| 7 | g535.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 303 | 329 | - |
| 4 | g535.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 305 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g535/g535.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g535.t6.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0055085 | transmembrane transport | BP |
| 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.
