Gene loci information

Transcript annotation

  • This transcript has been annotated as Copper-transporting ATPase 1.

Parent gene

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 g8628 g8628.t2 isoform g8628.t2 31917750 31923536
chr_2 g8628 g8628.t2 exon g8628.t2.exon1 31917750 31917849
chr_2 g8628 g8628.t2 cds g8628.t2.CDS1 31917750 31917849
chr_2 g8628 g8628.t2 exon g8628.t2.exon2 31918612 31918835
chr_2 g8628 g8628.t2 cds g8628.t2.CDS2 31918612 31918835
chr_2 g8628 g8628.t2 exon g8628.t2.exon3 31918896 31919074
chr_2 g8628 g8628.t2 cds g8628.t2.CDS3 31918896 31919074
chr_2 g8628 g8628.t2 exon g8628.t2.exon4 31919131 31919413
chr_2 g8628 g8628.t2 cds g8628.t2.CDS4 31919131 31919413
chr_2 g8628 g8628.t2 exon g8628.t2.exon5 31919471 31919638
chr_2 g8628 g8628.t2 cds g8628.t2.CDS5 31919471 31919638
chr_2 g8628 g8628.t2 exon g8628.t2.exon6 31919706 31920239
chr_2 g8628 g8628.t2 cds g8628.t2.CDS6 31919706 31920239
chr_2 g8628 g8628.t2 exon g8628.t2.exon7 31920466 31922557
chr_2 g8628 g8628.t2 cds g8628.t2.CDS7 31920466 31922557
chr_2 g8628 g8628.t2 exon g8628.t2.exon8 31923505 31923536
chr_2 g8628 g8628.t2 cds g8628.t2.CDS8 31923505 31923536
chr_2 g8628 g8628.t2 TSS g8628.t2 31923803 31923803
chr_2 g8628 g8628.t2 TTS g8628.t2 NA NA

Sequences

>g8628.t2 Gene=g8628 Length=3612
ATGGATGATGAAGAAAAAAATCCCACAAAAATTGATGCAATGGAAGAAGATCAAAGTCTT
TTAGATTTTCATGATACTGGTTCAACCAGTATCAATATTTATGGAATGAAGTGCCAAAAT
TGTGTTCGAAAAATTGAAGAAAATATGCAAAAAGAAATTGGAGTTTTGCAAATTAAAGTT
TATTTAGAAGAGAAACGAGCACAAATAGAATATGATAAACATGTGACAAATCCATTAGCA
TTGACAGCAGCAATTAAAAAATTGGGATTTCATACAAATCCAGATGATTTGAAGAAAATT
AAAGAATCAACTGTTTTCATAAATGGAATGAAGTGTAATAATTGTGTGAATAAAATTGAA
TCTTCAATAAAAGAAAAGAAAGGAATTGAGAAAATAAGTGTCGATTTGGCTAATAAAAGT
GCAATAGTGAAATATGATGAGTCAGCGACTAATTTAAGTGAAATTTTATCTCAAATAATT
CAGTTGGGTTTTAAAGCCAGTGATTCGCCATTTGATGAGAACATTGAAACTCAAAATGAC
TTAATTATAAATTTACCAGTGACTACAAACGGCAGTATCGAAAAAAATGATAAATTAATA
AGAAAAGGACACTTTCATGTACAAGGAATGACTTGTGCGAGTTGTGTATCAGCAATTGAA
AAACATTGCATGAAACTCAAAGGAGTTGAGACTGTTTTAATTTCTCTACTCGGTGCAAAA
GCTGAAATTTCATATGATGAGAATTTAATTGATGAAAATGAAATTGCAGCATCTTTAAGT
AGTTTAGGATTTCCAACAGAAGTCATTTATGAGCCAGAAGCAGGAATAAGTAGTATAGAA
ATTGAAATTCATGGAATGAGTTGTTCTTCATGTGTTAATAAAATTGAACAAGCTGTACTA
AAAATTAATGGCGTGATAAAAGCTTCTGTAGCGTTAACAACTCAACGTGGTAGATTTGAA
TATCATAATGAGCAAACAGGACCGCGTGAAATTTGTGAGAAAATTATCTCGCTTGGATTT
GAGGCGTCTGTGATAAGCAATCGAGATAAACTCTCGTATGGTTACTTGGAAAATAAACGC
GAGATTAAAAAATGGCGCGATACATTCCTCTTTTCACTTGCTTTTGGTGGTCCATGTATG
ATCGCTATGGCTTATTTTATGTTAATGATGGAAATTGAAGGACATGAAAGTATGTGCTGT
GTTGTCAGTGGCCTATCATTAGAGAATCTAGTCATGTTTGTTCTTTCAACTCCTGTTCAA
TTTATTGGCGGATACCATTTTTATGTTCAAGCTTATCGTGCAATTAAGCATGGATCAAGT
AATATGGATGTACTAATTAGTATGGCAACAATCATTAGCTATCTTTATTCAGTAATTGTT
TTAGCCATTGCAATGATTCAAAAGCATCATACTTCGCCATTAACATTTTTTGATACACCA
GCAATGCTTTTTATTTTTGTATCACTTGGTAGATGGCTTGAAAATATTGCAAGAGGCAAA
ACAAGTGAAGCACTTTCAAAACTCATGTCATTAAAACCAATCGATGCAATTATCGTGCAA
TTGGGAAAAGATAAAGAAATTTTAAGTGAAAAATCAATATCAGTTGATTTAATTCAACGT
GGTGACATTCTCAAAGTTATACCCGGAAGTAAAGTTCCAGTTGATGGAAAAATTATTTTT
GGCTCGAGTTCATGTGATGAAAGTTTGATAACTGGTGAATCAATGCCAGTGTTAAAGCGA
GAAGGTTCAATTGTAATTGGTGGATCAATAAATCAAAATGGATTGATTTTAATGACTGCA
ACACATACAGGTGAAAACACGACATTAGCACAAATTGTAAAATTAGTTGAAGAAGCACAA
ACGTCGAAAGCACCAATTCAACAATTAGCTGATAAAATCGCTGGATATTTTGTTCCTCTT
GTAATTTTAACATCGACTTTAACACTCTTTGGATGGTTGATTGCACTCAACATAAATATG
GATTGGCTGCCAAAAGCTGCTATGGAACATGGTGATTTCACAAATACAGAAATTATTTGG
AGTTTCTCTTTCAAATGTGCGATTTCTGTGCTTGCTATTGCTTGTCCTTGTGCACTTGGA
TTAGCTACTCCAACAGCTGTTATGGTTTCAACTGGCATTGGAGCATTAAATGGAATTTTA
ATAAAAGGGGCAAGTCCACTTGAGAATGCTCATAAAGTAAAGACAGTTGTATTTGACAAA
ACTGGCACAATAACACATGGGAAGCCTATGACTTCAAAGATTGTCATGTTTGTAAAACAA
GAAGTTTGTTCCTTAACACGAGCTTTAACCATAATAGGAAGTGCAGAAAGCTCTTCAGAG
CATCCGATTGCAAGAGCAATTGTCAGTTATATCAATGAGTTCCTTAAAATTGATTCCTTT
GGAAAATACTCAGATTTTACATCAGTTCCGGGTTGCGGAATACGATGTACAGTGTCGAAT
TTAGAAAAGACTTTTGCAACAGCATTGAGATCAGAAAAAGTTATAAACTTTGAAAATGCC
TATGAGAGCAACAGATCAAATGAAAAAATTATTCAAACAATCAATAATGTCACATTCGAG
GAACATTTACCAACGAATGTTAATAATTTATTACTCGAAAATGGATTGACAAATGAAAAT
GAAAGCATTTCAACGCATAGCAAAGTGAAAGTACTTATTGGAAACCGCGAATGGATGCAT
AGAAATGGAATAACAATACCTTCAGATATCAATCAAATTTTACTTGCTGAAGAATGTGTT
GGACATACAGCAGTTTTATGCTCACTTAATGATAAATTAATTTGCATGATTTCTGTTTCT
GATATGATCAAGCCTGAAGCACAATTAGCAGTCTATACTCTTAAGAAAATGAATATAAAT
GTCATCTTGTTGACTGGTGATAATAAAAATACAGCCAGTAGCATTGGTCAACAAGTTGGA
ATAAGAACAATTTATTCTGAAGTTCTTCCATCACATAAAGTAGCAAAAATACAAAAATTC
CAAGAAAGTGGAATGAGAGTTGCGATGGTTGGTGATGGAGTCAATGACTCACCAGCTTTA
GTACAAGCTGATGTTGGAATTGCTATTGGAAAAGGAACAGATGTTGCTGCTGAAGCTGCA
GATGTAGTGCTTATGAGAAATGATTTATTAGATGTTATTGCTTGCCTTGATTTATCACGT
AAGACTGTTAGAAGAATTAGAATGAATTTCTTATTTGCCAGTATGTACAATTTACTTGGA
ATTCCTATTGCTGCTGGGGTATTTAGTCCTTTTGGAATTTTGTTAGAGCCATGGATGGCA
GCTGCCGCAATGTGTGCAAGTTCGATTACTGTCGTATGCTCATCATTGATGTTGAAATTC
TATCGAAAGCCAACTGCAGCTTCACTCTCAACTCCTGAATTTAATAATTATCTTCAATCT
CTCAGCGATTTGGACGATATTTCTGTTCATCGAGGACTTGATGACATTCCTCGACCTGTT
TTTAATAGATCAAACAGTTCAATTATCTCAAGAATATTTACATCACTCAGAAGCAACAAT
TCAACGAAGGACTTGGACATTAAAACTCAACGCCTTTTATATGATGACGAAGATTTGAAT
TTTCATGTATAA

>g8628.t2 Gene=g8628 Length=1203
MDDEEKNPTKIDAMEEDQSLLDFHDTGSTSINIYGMKCQNCVRKIEENMQKEIGVLQIKV
YLEEKRAQIEYDKHVTNPLALTAAIKKLGFHTNPDDLKKIKESTVFINGMKCNNCVNKIE
SSIKEKKGIEKISVDLANKSAIVKYDESATNLSEILSQIIQLGFKASDSPFDENIETQND
LIINLPVTTNGSIEKNDKLIRKGHFHVQGMTCASCVSAIEKHCMKLKGVETVLISLLGAK
AEISYDENLIDENEIAASLSSLGFPTEVIYEPEAGISSIEIEIHGMSCSSCVNKIEQAVL
KINGVIKASVALTTQRGRFEYHNEQTGPREICEKIISLGFEASVISNRDKLSYGYLENKR
EIKKWRDTFLFSLAFGGPCMIAMAYFMLMMEIEGHESMCCVVSGLSLENLVMFVLSTPVQ
FIGGYHFYVQAYRAIKHGSSNMDVLISMATIISYLYSVIVLAIAMIQKHHTSPLTFFDTP
AMLFIFVSLGRWLENIARGKTSEALSKLMSLKPIDAIIVQLGKDKEILSEKSISVDLIQR
GDILKVIPGSKVPVDGKIIFGSSSCDESLITGESMPVLKREGSIVIGGSINQNGLILMTA
THTGENTTLAQIVKLVEEAQTSKAPIQQLADKIAGYFVPLVILTSTLTLFGWLIALNINM
DWLPKAAMEHGDFTNTEIIWSFSFKCAISVLAIACPCALGLATPTAVMVSTGIGALNGIL
IKGASPLENAHKVKTVVFDKTGTITHGKPMTSKIVMFVKQEVCSLTRALTIIGSAESSSE
HPIARAIVSYINEFLKIDSFGKYSDFTSVPGCGIRCTVSNLEKTFATALRSEKVINFENA
YESNRSNEKIIQTINNVTFEEHLPTNVNNLLLENGLTNENESISTHSKVKVLIGNREWMH
RNGITIPSDINQILLAEECVGHTAVLCSLNDKLICMISVSDMIKPEAQLAVYTLKKMNIN
VILLTGDNKNTASSIGQQVGIRTIYSEVLPSHKVAKIQKFQESGMRVAMVGDGVNDSPAL
VQADVGIAIGKGTDVAAEAADVVLMRNDLLDVIACLDLSRKTVRRIRMNFLFASMYNLLG
IPIAAGVFSPFGILLEPWMAAAAMCASSITVVCSSLMLKFYRKPTAASLSTPEFNNYLQS
LSDLDDISVHRGLDDIPRPVFNRSNSSIISRIFTSLRSNNSTKDLDIKTQRLLYDDEDLN
FHV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
56 g8628.t2 CDD cd00371 HMA 31 91 2.06241E-14
54 g8628.t2 CDD cd00371 HMA 107 167 1.11513E-14
53 g8628.t2 CDD cd00371 HMA 207 267 7.09425E-12
55 g8628.t2 CDD cd00371 HMA 280 343 1.31638E-14
52 g8628.t2 CDD cd02094 P-type_ATPase_Cu-like 369 1120 0.0
31 g8628.t2 Gene3D G3DSA:3.30.70.100 - 27 96 9.1E-16
32 g8628.t2 Gene3D G3DSA:3.30.70.100 - 98 167 4.1E-17
30 g8628.t2 Gene3D G3DSA:3.30.70.100 - 200 271 3.6E-19
29 g8628.t2 Gene3D G3DSA:3.30.70.100 - 277 349 2.7E-19
33 g8628.t2 Gene3D G3DSA:2.70.150.20 - 498 620 6.4E-45
34 g8628.t2 Gene3D G3DSA:3.40.1110.10 - 746 939 1.3E-56
8 g8628.t2 PANTHER PTHR43520:SF9 COPPER-TRANSPORTING ATPASE 2 31 168 0.0
10 g8628.t2 PANTHER PTHR43520 ATP7, ISOFORM B 31 168 0.0
7 g8628.t2 PANTHER PTHR43520:SF9 COPPER-TRANSPORTING ATPASE 2 188 1146 0.0
9 g8628.t2 PANTHER PTHR43520 ATP7, ISOFORM B 188 1146 0.0
16 g8628.t2 PRINTS PR00942 Copper-transporting ATPase 1 signature 39 57 4.0E-27
18 g8628.t2 PRINTS PR00942 Copper-transporting ATPase 1 signature 57 74 4.0E-27
17 g8628.t2 PRINTS PR00942 Copper-transporting ATPase 1 signature 369 390 4.0E-27
20 g8628.t2 PRINTS PR00942 Copper-transporting ATPase 1 signature 405 425 4.0E-27
19 g8628.t2 PRINTS PR00942 Copper-transporting ATPase 1 signature 425 450 4.0E-27
11 g8628.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 566 580 1.1E-25
12 g8628.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 737 751 1.1E-25
13 g8628.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 957 967 1.1E-25
15 g8628.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 1010 1029 1.1E-25
14 g8628.t2 PRINTS PR00119 P-type cation-transporting ATPase superfamily signature 1033 1045 1.1E-25
1 g8628.t2 Pfam PF00403 Heavy-metal-associated domain 32 91 9.5E-9
4 g8628.t2 Pfam PF00403 Heavy-metal-associated domain 104 165 2.9E-15
3 g8628.t2 Pfam PF00403 Heavy-metal-associated domain 205 264 4.8E-10
2 g8628.t2 Pfam PF00403 Heavy-metal-associated domain 281 341 3.0E-11
5 g8628.t2 Pfam PF00122 E1-E2 ATPase 529 712 6.2E-45
6 g8628.t2 Pfam PF00702 haloacid dehalogenase-like hydrolase 733 1024 7.5E-50
39 g8628.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 368 -
47 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 369 390 -
41 g8628.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 391 409 -
44 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 410 432 -
35 g8628.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 433 443 -
46 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 444 466 -
43 g8628.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 467 471 -
48 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 472 493 -
38 g8628.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 494 632 -
49 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 633 658 -
42 g8628.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 659 677 -
45 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 678 702 -
37 g8628.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 703 1069 -
50 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1070 1092 -
40 g8628.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1093 1097 -
51 g8628.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 1098 1118 -
36 g8628.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1119 1203 -
66 g8628.t2 ProSitePatterns PS01047 Heavy-metal-associated domain. 107 136 -
65 g8628.t2 ProSitePatterns PS01047 Heavy-metal-associated domain. 283 312 -
67 g8628.t2 ProSitePatterns PS00154 E1-E2 ATPases phosphorylation site. 739 745 -
76 g8628.t2 ProSiteProfiles PS50846 Heavy-metal-associated domain profile. 28 94 18.656
75 g8628.t2 ProSiteProfiles PS50846 Heavy-metal-associated domain profile. 102 168 19.318
74 g8628.t2 ProSiteProfiles PS50846 Heavy-metal-associated domain profile. 202 268 18.968
77 g8628.t2 ProSiteProfiles PS50846 Heavy-metal-associated domain profile. 278 344 19.685
78 g8628.t2 SFLD SFLDF00027 p-type atpase 719 1062 0.0
79 g8628.t2 SFLD SFLDS00003 Haloacid Dehalogenase 719 1062 0.0
24 g8628.t2 SUPERFAMILY SSF55008 HMA, heavy metal-associated domain 27 94 1.57E-13
25 g8628.t2 SUPERFAMILY SSF55008 HMA, heavy metal-associated domain 100 167 1.28E-16
23 g8628.t2 SUPERFAMILY SSF55008 HMA, heavy metal-associated domain 203 269 1.26E-15
22 g8628.t2 SUPERFAMILY SSF55008 HMA, heavy metal-associated domain 274 347 4.84E-17
26 g8628.t2 SUPERFAMILY SSF81665 Calcium ATPase, transmembrane domain M 454 1109 5.89E-7
27 g8628.t2 SUPERFAMILY SSF81653 Calcium ATPase, transduction domain A 531 616 1.57E-23
28 g8628.t2 SUPERFAMILY SSF56784 HAD-like 735 1115 3.52E-51
21 g8628.t2 SUPERFAMILY SSF81660 Metal cation-transporting ATPase, ATP-binding domain N 766 820 2.68E-6
72 g8628.t2 TIGRFAM TIGR00003 TIGR00003: copper ion binding protein 31 91 4.3E-9
71 g8628.t2 TIGRFAM TIGR00003 TIGR00003: copper ion binding protein 104 165 2.4E-11
69 g8628.t2 TIGRFAM TIGR00003 TIGR00003: copper ion binding protein 203 264 2.3E-10
70 g8628.t2 TIGRFAM TIGR00003 TIGR00003: copper ion binding protein 279 342 1.2E-10
73 g8628.t2 TIGRFAM TIGR01525 ATPase-IB_hvy: heavy metal translocating P-type ATPase 442 1118 4.7E-189
68 g8628.t2 TIGRFAM TIGR01494 ATPase_P-type: HAD ATPase, P-type, family IC 917 1087 9.4E-41
63 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 368 390 -
58 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 410 432 -
59 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 444 466 -
61 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 476 493 -
57 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 633 655 -
60 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 678 700 -
62 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 1070 1092 -
64 g8628.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 1096 1118 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0046872 metal ion binding MF
GO:0019829 ATPase-coupled cation transmembrane transporter activity MF
GO:0005507 copper ion binding MF
GO:0000166 nucleotide binding MF
GO:0016021 integral component of membrane CC
GO:0006812 cation transport BP

KEGG

Orthology

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.

Raw TPM values