General information for g535.t5
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.t5 | TSS | g535.t5 | 3970722 | 3970722 |
| chr_3 | g535 | g535.t5 | isoform | g535.t5 | 3970971 | 3974238 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon1 | 3970971 | 3971046 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon2 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t5 | cds | g535.t5.CDS1 | 3972717 | 3972892 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon3 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t5 | cds | g535.t5.CDS2 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon4 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t5 | cds | g535.t5.CDS3 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon5 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t5 | cds | g535.t5.CDS4 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t5 | exon | g535.t5.exon6 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t5 | cds | g535.t5.CDS5 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t5 | TTS | g535.t5 | NA | NA |
Sequences
>g535.t5 Gene=g535 Length=985
ATGGAGAATTGTGAATATAGCATTATTGGAACGGGTCGTCAAGTAGGAGGTAAAAATAAT
AATAAATTGATAAAAAGCCAAATTTAGACTGTTGATGTGGAAAAATTACCTTCTTCAGTA
TCGTCATCCATTTCAAACAATTCTTGAGATTGCTATACCAGTATTATTTTCAGCATTACT
CGTACTCATTCGTAGCTTAGTATCACCCGACATTTTTTCAGATCCAACGATCTATCCACC
TTTACCATTAACTGATATCAAACAGACCTTTGGCGCTAGAGGAGAGTTTGCTTTCAAAGT
TCTCTCATTTAACAAGAACATCAATATTTCACAATTTACAAACTTTTCTAATGAAATCGT
CTACTCACCGGATAACATTGAAGTCAATGCATTGATGAAAGAGTTAAATAGTTATGTGAA
ACCTTTCCTTAAGGTCACTCCTGTGCCTTCATCAAATGAACTAGCTCCGTACTTAAGAAA
ATCAAATGCTTATGTTGGAATTGAATTTCCTGATAACTATAAAAACATAACAGAACTACC
AGATGATCTCGAATACAGTATACGATATCCAGGAGAATTACGAAGAACAGGAGGAGCTTT
AAATCCATTATTTTTCAACTGGCGAACAGATTTTCTTTTTCCACTTTTTCAACCGGGTGG
CTCGAGAAATTTCAACAACACTCATGACGGATTGCCTAGTGGCTATTATATTGAAGGATT
TTTATTTGTTCAACAATTTATGTTTAAAGCTTTCTCGACTTTGAAAAATAAAATGGACAT
TGACCTAAAACAATTACCAAAAATCAATATAAGGAGATTTCCTTATCCACCTTTTGTTCT
TGATATATTACTGCAGGGACTTCAATCACTTGTTTCACTTTTTATCTTGCTAAGTTTTGT
TTATCCTTGCATTAACATCATCAAGTACATCACAACTGAAAAAGAAAAACAACTAAAAGA
AGCTATGAAAATTATGGGATTAGAT
>g535.t5 Gene=g535 Length=297
MWKNYLLQYRHPFQTILEIAIPVLFSALLVLIRSLVSPDIFSDPTIYPPLPLTDIKQTFG
ARGEFAFKVLSFNKNINISQFTNFSNEIVYSPDNIEVNALMKELNSYVKPFLKVTPVPSS
NELAPYLRKSNAYVGIEFPDNYKNITELPDDLEYSIRYPGELRRTGGALNPLFFNWRTDF
LFPLFQPGGSRNFNNTHDGLPSGYYIEGFLFVQQFMFKAFSTLKNKMDIDLKQLPKINIR
RFPYPPFVLDILLQGLQSLVSLFILLSFVYPCINIIKYITTEKEKQLKEAMKIMGLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g535.t5 | PANTHER | PTHR19229:SF139 | ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 14 | 1 | 296 | 5.5E-31 |
| 3 | g535.t5 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 1 | 296 | 5.5E-31 |
| 1 | g535.t5 | Pfam | PF12698 | ABC-2 family transporter protein | 15 | 296 | 1.3E-8 |
| 8 | g535.t5 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 10 | g535.t5 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 7 | g535.t5 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 33 | 246 | - |
| 11 | g535.t5 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 247 | 270 | - |
| 9 | g535.t5 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 271 | 297 | - |
| 5 | g535.t5 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 6 | g535.t5 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 200 | 217 | - |
| 4 | g535.t5 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 273 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g535/g535.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g535.t5.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.
