General information for g535.t1
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 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.t1 | TSS | g535.t1 | 3970722 | 3970722 |
| chr_3 | g535 | g535.t1 | isoform | g535.t1 | 3970971 | 3975754 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS1 | 3970971 | 3971019 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS2 | 3972602 | 3972630 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS3 | 3972699 | 3972892 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS4 | 3972963 | 3973001 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon5 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS5 | 3973444 | 3973657 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon6 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS6 | 3973718 | 3974008 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon7 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS7 | 3974068 | 3974238 |
| chr_3 | g535 | g535.t1 | exon | g535.t1.exon8 | 3974411 | 3975754 |
| chr_3 | g535 | g535.t1 | cds | g535.t1.CDS8 | 3974411 | 3975754 |
| chr_3 | g535 | g535.t1 | TTS | g535.t1 | NA | NA |
Sequences
>g535.t1 Gene=g535 Length=2331
ATGGAGAATTGTGAATATAGCATTATTGGAACGGGTCGTCAAGTAGGAGACTCAGACGTT
AGGATGACATCGAAATGGGCCAAATTTAGACTGTTGATGTGGAAAAATTACCTTCTTCAG
TATCGTCATCCATTTCAAACAATTCTTGAGATTGCTATACCAGTATTATTTTCAGCATTA
CTCGTACTCATTCGTAGCTTAGTATCACCCGACATTTTTTCAGATCCAACGATCTATCCA
CCTTTACCATTAACTGATATCAAACAGACCTTTGGCGCTAGAGGAGAGTTTGCTTTCAAA
GTTCTCTCATTTAACAAGAACATCAATATTTCACAATTTACAAACTTTTCTAATGAAATC
GTCTACTCACCGGATAACATTGAAGTCAATGCATTGATGAAAGAGTTAAATAGTTATGTG
AAACCTTTCCTTAAGGTCACTCCTGTGCCTTCATCAAATGAACTAGCTCCGTACTTAAGA
AAATCAAATGCTTATGTTGGAATTGAATTTCCTGATAACTATAAAAACATAACAGAACTA
CCAGATGATCTCGAATACAGTATACGATATCCAGGAGAATTACGAAGAACAGGAGGAGCT
TTAAATCCATTATTTTTCAACTGGCGAACAGATTTTCTTTTTCCACTTTTTCAACCGGGT
GGCTCGAGAAATTTCAACAACACTCATGACGGATTGCCTAGTGGCTATTATATTGAAGGA
TTTTTATTTGTTCAACAATTTATGTTTAAAGCTTTCTCGACTTTGAAAAATAAAATGGAC
ATTGACCTAAAACAATTACCAAAAATCAATATAAGGAGATTTCCTTATCCACCTTTTGTT
CTTGATATATTACTGCAGGGACTTCAATCACTTGTTTCACTTTTTATCTTGCTAAGTTTT
GTTTATCCTTGCATTAACATCATCAAGTACATCACAACTGAAAAAGAAAAACAACTAAAA
GAAGCTATGAAAATTATGGGATTAGATAGTTGGCTTCATTGGATTGCATGGTTTACCAAA
TGTTTTATCTACATGCTAATCACAGTCACATTTATGACAATTTTGATGAAGGTCAAATGG
TATGGTGAAGATAATCCAAATTCAGTCTTCACCTATAGTTCAGCAACAGTTTTATGGACA
TTTTTACTTCTCTATAGCATCACAACGATCATGTTTTGTTTCATGCTCAGTGTATTTTTC
TCAAAAGCTTCAACAGCTGCTGCTGTAGCTGGATTGGTTTGGTTTCTGATTTACTCACCC
TATTCTTTCATACAACAACGTTATGACTCAATTTCATTAACGACAAAAATCCTACTGAGT
TTTATGTCCAACACAGGCATGGCGTTGGGTTTTAATGTGATTATGCGGTATGAAGGAACA
CAGGAAGGCATGCAATGGCATAACATCTTCAAACCAGTGTCAATCGATGATACATTTCAT
CTTGGGCATGTGATTATAATGTTGATTGTTGATGCCATCATTTATCTGCTGATTGCACTT
TATGTTGAGAAAATTTTTCCTGGTGATTATGGAGTAGCAGAAAAATGGAATTTTCCATTT
TCATCAAAATTTTGGTTTAAAGTTCCTGAATATGTTGGAGTTCGTGATGTGAATTCGAAT
GATGTAAATCATTTAAATCCTAATTATGAACACGAACCAAAAAATAAAGCTGCTGGCATT
CAAATTTACAATTTAAGGAAAACTTTTGACAATAATCGTGTGGCAGTTGAAGGTTTAAAT
TTAAACATGTATGAAGATCAAATCACTGTTCTACTTGGGCATAATGGAGCAGGCAAAACA
ACAACAATGTCGATGGTAACTGGAATGATTCAACCAACTTCAGGAACAGCAATTATCAAT
GGAAAAGATATCAGAAGGGATATGAATGCAATTCGATCTTCAATTGGTTTTTGTCCTCAA
CATAACATTCTATTTGAAGATTTAACAGTTCGTGAGCACATCACATTTTATAGTTTACTC
AAAGGATTGCACAAAGATGATGTTGAAAGAGAAGTCGAGAAATATGTAAAATTATTGAAA
CTCGAAAACAAAATTGATGTGCAAGCTAGTGGACTATCTGGTGGAATGAAACGAAAGCTG
TCAGTTGGTATTGCTCTTTGTGCAAATTCAAAAATTGTTTTATTTGATGAACCAAGCTCA
GGTGTTGATCCTGGTGCGAGAAGAGACTTGTGGGACTTGTTACAAGCTGAAAAAGGTGGT
CGAACTATTTTATTATCAACTCATTTCATGCTCGAAGCAGATGTGCTTGGTGATCGCATT
GCAATCATGTCTAATGGAGTTCTTAAAGCTGTTGGTTCACCANTTACTTGA
>g535.t1 Gene=g535 Length=776
MENCEYSIIGTGRQVGDSDVRMTSKWAKFRLLMWKNYLLQYRHPFQTILEIAIPVLFSAL
LVLIRSLVSPDIFSDPTIYPPLPLTDIKQTFGARGEFAFKVLSFNKNINISQFTNFSNEI
VYSPDNIEVNALMKELNSYVKPFLKVTPVPSSNELAPYLRKSNAYVGIEFPDNYKNITEL
PDDLEYSIRYPGELRRTGGALNPLFFNWRTDFLFPLFQPGGSRNFNNTHDGLPSGYYIEG
FLFVQQFMFKAFSTLKNKMDIDLKQLPKINIRRFPYPPFVLDILLQGLQSLVSLFILLSF
VYPCINIIKYITTEKEKQLKEAMKIMGLDSWLHWIAWFTKCFIYMLITVTFMTILMKVKW
YGEDNPNSVFTYSSATVLWTFLLLYSITTIMFCFMLSVFFSKASTAAAVAGLVWFLIYSP
YSFIQQRYDSISLTTKILLSFMSNTGMALGFNVIMRYEGTQEGMQWHNIFKPVSIDDTFH
LGHVIIMLIVDAIIYLLIALYVEKIFPGDYGVAEKWNFPFSSKFWFKVPEYVGVRDVNSN
DVNHLNPNYEHEPKNKAAGIQIYNLRKTFDNNRVAVEGLNLNMYEDQITVLLGHNGAGKT
TTMSMVTGMIQPTSGTAIINGKDIRRDMNAIRSSIGFCPQHNILFEDLTVREHITFYSLL
KGLHKDDVEREVEKYVKLLKLENKIDVQASGLSGGMKRKLSVGIALCANSKIVLFDEPSS
GVDPGARRDLWDLLQAEKGGRTILLSTHFMLEADVLGDRIAIMSNGVLKAVGSPXT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g535.t1 | CDD | cd03263 | ABC_subfamily_A | 560 | 774 | 9.08486E-113 |
| 6 | g535.t1 | Gene3D | G3DSA:3.40.50.300 | - | 548 | 776 | 1.8E-62 |
| 3 | g535.t1 | PANTHER | PTHR19229:SF36 | ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 3B | 26 | 775 | 2.5E-203 |
| 4 | g535.t1 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 26 | 775 | 2.5E-203 |
| 1 | g535.t1 | Pfam | PF12698 | ABC-2 family transporter protein | 48 | 501 | 1.2E-25 |
| 2 | g535.t1 | Pfam | PF00005 | ABC transporter | 577 | 719 | 3.0E-28 |
| 12 | g535.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 44 | - |
| 15 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 9 | g535.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 290 | - |
| 17 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 311 | - |
| 14 | g535.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 312 | 330 | - |
| 21 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 331 | 356 | - |
| 8 | g535.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 357 | 376 | - |
| 16 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 377 | 400 | - |
| 11 | g535.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 401 | 405 | - |
| 19 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 424 | - |
| 7 | g535.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 425 | 435 | - |
| 20 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 436 | 455 | - |
| 13 | g535.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 456 | 480 | - |
| 18 | g535.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 481 | 502 | - |
| 10 | g535.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 503 | 776 | - |
| 29 | g535.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 692 | 706 | - |
| 31 | g535.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 560 | 776 | 18.861 |
| 30 | g535.t1 | SMART | SM00382 | AAA_5 | 585 | 767 | 2.3E-8 |
| 5 | g535.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 560 | 774 | 2.66E-53 |
| 28 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 313 | - |
| 24 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 334 | 356 | - |
| 26 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 376 | 398 | - |
| 23 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 405 | 424 | - |
| 27 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 437 | 459 | - |
| 25 | g535.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 480 | 502 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g535/g535.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g535.t1.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 |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01990 (ABC-2 type 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.
