General information for g539.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 g539 is located on chr_3: 3984336..3988475 (+ 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 | g539 | g539.t1 | isoform | g539.t1 | 3984336 | 3988475 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon1 | 3984336 | 3984350 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS1 | 3984336 | 3984350 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon2 | 3984411 | 3984604 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS2 | 3984411 | 3984604 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon3 | 3984979 | 3985186 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS3 | 3984979 | 3985186 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon4 | 3985247 | 3985534 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS4 | 3985247 | 3985534 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon5 | 3985589 | 3985759 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS5 | 3985589 | 3985759 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon6 | 3985932 | 3987541 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS6 | 3985932 | 3987541 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon7 | 3987594 | 3988134 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS7 | 3987594 | 3988134 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon8 | 3988190 | 3988330 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS8 | 3988190 | 3988330 |
| chr_3 | g539 | g539.t1 | exon | g539.t1.exon9 | 3988389 | 3988475 |
| chr_3 | g539 | g539.t1 | cds | g539.t1.CDS9 | 3988389 | 3988475 |
| chr_3 | g539 | g539.t1 | TSS | g539.t1 | NA | NA |
| chr_3 | g539 | g539.t1 | TTS | g539.t1 | NA | NA |
Sequences
>g539.t1 Gene=g539 Length=3255
ATGACGTCTAAATGGGCCAAATTTAGACTGCTAATGTGGAAAAATTATCTTCTTCAACGT
CGACATCCATTTCAAACGATTCTTGAGATTTCTATACCAGTATTATTTGCAACATTGCTG
GTACTCATTCGTAGCTTAGTATCACCCGAAATCTTCTCAGTTCCGACGATCTATCCACCT
CTGCCATTGCATAATTTTCATCAACACTTTACTAAACTTAACAATTATCAATTTTTAAAA
TACACATATGAAATTGCTTATTCACCGCAAAATAATGAAATTGATAAGTTAATGGAAGTA
TTCAAGAAAGACACAAGAACAGAAAATGTCACTGCATTAGCTTCATCAGCTGATCTTGAA
TTGCATATGATAAAATCACACACTTATTTTGGAATAGAATTTCCTGATGAATACAAATTT
TTAAAAGAATTACCAGATAATATCGAATACAGTATCCGATTTCCAGCAGAATTACGCAGA
ACCAATTGGGAAGTAAATATTTACTATAACTGGCACACAGATACACTTTTCCCTTTTAAA
CAATTTGGAGGTGCAAGAAATTCTCATGTTTCTCATGATGGCGTACCTAGTGGCTATTAC
ATTGAAGGATTTTTATCAGCACAAGAATTTCTATTCAAAGCTTTTTCACGTTATAAGAAT
AAAATGAACATTGACTTAAATCTATTTCCAAAAATCAAAATGAGAAAATTTCCCTATCCT
CCATTCGTTTATGATGGTCTCTTACAAGCTCTTGAAATTATTGTTGCACTCTTTTTTCTT
TTGAGTTTTATCTATCCGTGTGTTAACTTTGTCAAACAGATTACAATTGAAAAAGAAAAA
CAGCTGAAAGAAGCTATGAAAATTATGGGATTAGATAGTTGGCTTCATTGGACTGCATGG
TTTACTAAATGTTTTATCTACATGCTAATCACAGTCACATTTATGACAATTTTGATGAAG
GTCAAATGGTATGGTGAAGATAATCCAAATTCAGTCTTCACCTATAGTTCAGCAACAGTT
TTATGGACATTTTTACTTCTCTATAGCATCACAACGATCATGTTTTGTTTCATGCTCAGT
GTATTCTTCTCAAAAGCGGATATTGCTGCTGCTGTTTCAGGACTTGTCTTTTTTCTCATT
TATTGTCCTTATTCATTGATTATCATGAATTATGATCTGATTTCAATGAAATTGAAAGTT
GTAATGTGTTTGTTTTTAAATACAGGCATGGCGTTGGGAATTGATATAATTTTACGTTAT
GAAGGAACACAGGAAGGCATGCAATGGCATAACATCTTCAAACCAGTCTCAGTCAATGAT
ACTTTTCATCTTGGGCATGTGATTATAATGTTGATTGTTGATGCCATCATTTATCTGCTA
ATTGCACTTTATGTTGAGAAAATTTTTCCTGGTGATTATGGAGTAGCAGAAAAATGGAAT
TTTCCATTTTCATCAAAATTTTGGTTTAAAGTTCCTGAATATGTTGGAGTTCGTGATGTG
AATTCGAATGATGTAAATCATTTAAATCCTAATTATGAACATCAACCAAAAAATAAAGCT
GCTGGCATTCAAATTTACAATTTAAGGAAAACTTTTGACAATAATCGTGTGGCAGTTGAA
GGTTTAAATTTAAACATGTATGAAGATCAAATCACTGTTCTACTTGGGCATAATGGAGCA
GGCAAAACAACAACAATGTCGATGGTAACTGGAATGATTCAACCAACTTCAGGAACAGCA
ATTATCAATGGAAAAGATATCAGAAGAGATATGAATGCAATTCGATCTTCAATTGGTTTT
TGTCCTCAACATAACATTCTTTTTGAAGATTTAACAGTTCGTGAGCACATCACATTTTAT
AGCTTGCTCAAAGGATTGCACAAAGATGATGTTGAAAGAGAAGTCGAAAAATATGTAAAA
TTATTGAAACTCGAAAACAAAATTGATGTGCAAGCTAGTGGACTATCTGGTGGAATGAAA
CGAAAACTGTCAGTTGGTATTGCTCTTTGTGCAAATTCAAAAATTGTTTTATTTGATGAA
CCAAGCTCAGGTGTTGATCCTGGTGCGAGAAGAGACTTGTGGGACTTGTTACAAGCTGAA
AAAGGTGGTCGAACTATTTTATTATCAACTCATTTCATGCTCGAAGCAGATGTGCTTGGT
GATCGCATTGCAATCATGTCTAATGGAGTTCTTAAAGCTGTTGGTTCACCATATTTTCTC
AAGAAACAATTTGGTGTTGGCTATCATTTAGTTTGTGTCAAAAAAGATGCTTCATGTGAT
TCAATGGCAGTTACTGAATTATTGAGAAAATACATTCCAGATGTGAAGAAAGAAAGTGAA
ATTGGCACTGAATTGTCTTATTTACTTGATGATAAAAATGTACTGGTGTTTCAAAAGATG
TTGAAAGAACTTGAAGAAAATTCAAAAGAATTGAATATCGAAAGTTATGGAATTTCATTG
ACAACACTTGAAGAAGTTTTCTTAAAAGTTGGAACAGATAATTTGGAAGATGAATCAAAA
CCATCTACAAAATTAAATGGAACTACAACATCAAATAAATATGAAAATGAAATTGAGAAT
GGCTTAGATTCGAATACATTTTTAGTTCACAAAGGAGCTCAGTTATATCTCAATCAGTTT
GTTGCACTTATGCATAAAAAAGTTCTTTTATCATGGAGAAATTTGCTACTTATAGTTATT
CAAATGATCATCCCCATAGCTTTTGTTTCAGTCCTAATGTGCTCCTTTAAAGCTTTGTAT
GAAAATAAGAATTTACCAAAATTAGATTTGACAATGGACACTTATAAGCCATCAGTCACA
ACAATAGAATTTCGATCATCTGATCAAAGTGAAACAATTGAAAACAAGATATTTGAAAAT
TATCGAAAGCAATTCAGTGATTTGACATCACTTGAAATCATTCATGATGATATGATTGAA
CATTATCTCAATAAATCTAAAAAATATTTAGCTCGTGTCAATAATGAATATCTTTTTGGT
GCAACAATTGAAAAATCAAGTATAACTGTGTGGTTCAATAATCAACCTTATCATACAAGT
CCCATTAGCTTATCACTCGTGCATAATGCAATGTTACGAACAATTTGTGGTGAAAATTGT
AGCATAAAAGTGTCAAACAAACCATTGCCTTATGGTGCTGAATCGATAGTGATGATGCTT
CAAGCTGGTAAAAATCTTGGCTTTCAATTAGCTTTTAACATTGGATTTGCGATGGCGTTG
CTTCATTCTTTGTAA
>g539.t1 Gene=g539 Length=1084
MTSKWAKFRLLMWKNYLLQRRHPFQTILEISIPVLFATLLVLIRSLVSPEIFSVPTIYPP
LPLHNFHQHFTKLNNYQFLKYTYEIAYSPQNNEIDKLMEVFKKDTRTENVTALASSADLE
LHMIKSHTYFGIEFPDEYKFLKELPDNIEYSIRFPAELRRTNWEVNIYYNWHTDTLFPFK
QFGGARNSHVSHDGVPSGYYIEGFLSAQEFLFKAFSRYKNKMNIDLNLFPKIKMRKFPYP
PFVYDGLLQALEIIVALFFLLSFIYPCVNFVKQITIEKEKQLKEAMKIMGLDSWLHWTAW
FTKCFIYMLITVTFMTILMKVKWYGEDNPNSVFTYSSATVLWTFLLLYSITTIMFCFMLS
VFFSKADIAAAVSGLVFFLIYCPYSLIIMNYDLISMKLKVVMCLFLNTGMALGIDIILRY
EGTQEGMQWHNIFKPVSVNDTFHLGHVIIMLIVDAIIYLLIALYVEKIFPGDYGVAEKWN
FPFSSKFWFKVPEYVGVRDVNSNDVNHLNPNYEHQPKNKAAGIQIYNLRKTFDNNRVAVE
GLNLNMYEDQITVLLGHNGAGKTTTMSMVTGMIQPTSGTAIINGKDIRRDMNAIRSSIGF
CPQHNILFEDLTVREHITFYSLLKGLHKDDVEREVEKYVKLLKLENKIDVQASGLSGGMK
RKLSVGIALCANSKIVLFDEPSSGVDPGARRDLWDLLQAEKGGRTILLSTHFMLEADVLG
DRIAIMSNGVLKAVGSPYFLKKQFGVGYHLVCVKKDASCDSMAVTELLRKYIPDVKKESE
IGTELSYLLDDKNVLVFQKMLKELEENSKELNIESYGISLTTLEEVFLKVGTDNLEDESK
PSTKLNGTTTSNKYENEIENGLDSNTFLVHKGAQLYLNQFVALMHKKVLLSWRNLLLIVI
QMIIPIAFVSVLMCSFKALYENKNLPKLDLTMDTYKPSVTTIEFRSSDQSETIENKIFEN
YRKQFSDLTSLEIIHDDMIEHYLNKSKKYLARVNNEYLFGATIEKSSITVWFNNQPYHTS
PISLSLVHNAMLRTICGENCSIKVSNKPLPYGAESIVMMLQAGKNLGFQLAFNIGFAMAL
LHSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g539.t1 | CDD | cd03263 | ABC_subfamily_A | 523 | 741 | 6.85288E-111 |
| 7 | g539.t1 | Coils | Coil | Coil | 794 | 814 | - |
| 6 | g539.t1 | Gene3D | G3DSA:3.40.50.300 | - | 511 | 754 | 1.5E-63 |
| 3 | g539.t1 | PANTHER | PTHR19229:SF139 | ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 14 | 6 | 1083 | 5.5E-246 |
| 4 | g539.t1 | PANTHER | PTHR19229 | ATP-BINDING CASSETTE TRANSPORTER SUBFAMILY A ABCA | 6 | 1083 | 5.5E-246 |
| 1 | g539.t1 | Pfam | PF12698 | ABC-2 family transporter protein | 26 | 464 | 6.9E-23 |
| 2 | g539.t1 | Pfam | PF00005 | ABC transporter | 540 | 682 | 5.0E-28 |
| 16 | g539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 23 | - |
| 18 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 43 | - |
| 9 | g539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 44 | 241 | - |
| 21 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 265 | - |
| 13 | g539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 266 | 296 | - |
| 23 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 319 | - |
| 8 | g539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 320 | 339 | - |
| 20 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 362 | - |
| 15 | g539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 363 | 367 | - |
| 19 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 368 | 388 | - |
| 11 | g539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 389 | 399 | - |
| 17 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 420 | - |
| 12 | g539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 421 | 443 | - |
| 24 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 444 | 465 | - |
| 10 | g539.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 466 | 894 | - |
| 22 | g539.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 895 | 920 | - |
| 14 | g539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 921 | 1084 | - |
| 35 | g539.t1 | ProSitePatterns | PS00211 | ABC transporters family signature. | 655 | 669 | - |
| 36 | g539.t1 | ProSiteProfiles | PS50893 | ATP-binding cassette, ABC transporter-type domain profile. | 523 | 753 | 21.555 |
| 34 | g539.t1 | SMART | SM00382 | AAA_5 | 548 | 730 | 2.3E-8 |
| 5 | g539.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 515 | 749 | 1.98E-54 |
| 29 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 27 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
| 30 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 319 | - |
| 32 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 339 | 361 | - |
| 31 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 368 | 390 | - |
| 33 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 422 | - |
| 26 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 465 | - |
| 28 | g539.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 890 | 912 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g539/g539.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g539.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 K05643 (ATP-binding cassette, subfamily A (ABC1), member 3)
Pathway
- This transcript belongs to the following 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.
