Gene loci information

Transcript annotation

  • This transcript has been annotated as AFG3-like protein 2.

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 g6701 g6701.t5 isoform g6701.t5 18109855 18113220
chr_2 g6701 g6701.t5 exon g6701.t5.exon1 18109855 18110228
chr_2 g6701 g6701.t5 exon g6701.t5.exon2 18110429 18110646
chr_2 g6701 g6701.t5 cds g6701.t5.CDS1 18110551 18110646
chr_2 g6701 g6701.t5 exon g6701.t5.exon3 18110719 18111173
chr_2 g6701 g6701.t5 cds g6701.t5.CDS2 18110719 18111173
chr_2 g6701 g6701.t5 exon g6701.t5.exon4 18111230 18111622
chr_2 g6701 g6701.t5 cds g6701.t5.CDS3 18111230 18111622
chr_2 g6701 g6701.t5 exon g6701.t5.exon5 18111683 18111816
chr_2 g6701 g6701.t5 cds g6701.t5.CDS4 18111683 18111816
chr_2 g6701 g6701.t5 exon g6701.t5.exon6 18111881 18113220
chr_2 g6701 g6701.t5 cds g6701.t5.CDS5 18111881 18113220
chr_2 g6701 g6701.t5 TTS g6701.t5 18113191 18113191
chr_2 g6701 g6701.t5 TSS g6701.t5 NA NA

Sequences

>g6701.t5 Gene=g6701 Length=2914
TGATACAAATTTTAAAAATAAAGAATATCGTTATTTACATTTCTACTGTAACTTAGCTTG
TTATTCATCAGTATATTGATTTATTAATTTTTTTTATCAATTCTATACATCAGTTTTTTA
TTGCAGATTAATATCTAAGTTAAGAGATTTGTTCATTTAAAATCAAAACTTCATTTTTAC
AGAAAACAAGTACAGAGCGATTTTTTCGATTTTGGATTATTCAGAGAATTGACCTTATTT
TATATTTTAAACAATTCAGTTAGTCGCGAGATTGTATTGTTAAAATTATGTGCAGTGTTA
GCAATTTCATTTTTGACCTATTTTTACAAAAATTTTTTAAAAGATGAAAAATGGAGATTT
TACGCAAAAGAAAGAAATATTTCCTATAAGTTTGCCGTGCGAAATTTTTGTTGTGCCTTA
AGTTGATTTCCCCTTGATAAAATTAAATAACAACATAGAATTTTGTAGAAAGCAAAATAA
TTATTATAGGATAAATATGGCTTATAGATTAATAACAACAACTTGTAATAAACAATTGGA
AAGAACTCTTCTAAGTTCTATTAAAAGTCGCCATTTATCAGTTAATTTGAAATCAAAACA
TGATTTAGCATTTATAACAAGAAATAGTGACAAACCTTCTATTCTTGAAATATTTTTAAA
TGAATTGAGAATATTAACATCAAGCGATGGTCCAAAAGATAAATTCTTCAAACCTCCAAA
ATCAACATCAAATTCACAGCCATCATCGTCTGAATCAAACGAAAATCCGCCACAAAAACC
CACTAAACCTTCAACTTCTTCAACAAACAATAGCAATAATAAATCACCACCTGATTGGAA
TTTAGGAATGTTTTCTCCTAATCCATCTGCAGGTCCTAAAAATAATAGCGGCAGTTCTCA
AGGAAGGCCTATCGGAGGTGGTGATCCTAATCCAGAACAAAATAAAATGCTATTCTATGG
TGCACTTGGATTTGCTGCAGTAATTATTGCATTGACATACTTTGAAATGGGTTATAAGGA
AATTTCATGGAGAGATTTCATAAATAATTATCTAGGTCGTGGTGTTGTAGAGCGATTAGA
AGTCATCAACAAAAAATGGGTTCGAGTTAAATTAATGCCTGGAAATGTTAGTGATGGTGT
ATTATGGTTTAATATTGGTAGCGTGGATTCTTTCGAACGAAATTTAGAGAATGCACAAGC
TGATCTCAATATAGAACCGGCAAATTATATTCCAGTTATATATAAATCTGAAATTGAAGC
CGCTAATTTAACAGGGCTTTTGCCGACTCTTCTCATTATTGGTTTCTTAATATATATGAT
GCGTCGTTCCGCTGATATGATGGGTGGAGGAAGAGGCAGAAAAGGAGGTGGTCTTTTCGG
CGGAGTAATGCAATCAACTGCAAGATTAATTAATCCTAATGAAATCGGAGTCAAATTTAC
TGATGTTGCTGGATGTGAAGAAGCTAAGATTGAGATCATGGAATTTGTAAATTTTTTGAA
AAATCCTCAACAATACATTGACTTGGGTGCAAAAATTCCAAAAGGTGCTTTGTTAACCGG
ACCACCTGGCACAGGTAAAACTTTGTTGGCAAAAGCAACTGCAGGCGAGGCAAATGTTCC
ATTCATCACTGTTTCTGGTAGTGAATTTTTAGAAATGTTTGTCGGTGTCGGTCCATCACG
AGTTCGTGATATGTTTGCTATGGCACGAAAGCAAGCTCCATGTATACTTTTTATTGATGA
GATTGATGCAGTTGGTAGAAAGCGTGGTGGCAAATCATTCGGAGGTCACTCAGAACAAGA
AAACACGTTAAATCAGCTTTTAGTAGAGATGGATGGATTTAATACAACAACAAATGTCGT
TGTTTTAGCTGCTACAAATCGCTTAGACATATTAGATAAGGCATTGCTTAGACCAGGCAG
ATTCGATCGTCAAATATTTGTTCCTGCGCCTGATATCAAAGGTCGTGCATCAATTTTCAA
AGTACATTTGGCTAATCTTAAAACAGATTTAGATAAAGTTGAACTTGCACGAAAAATGGC
TGCATTAACTCCTGGTTTCACTGGTGCTGATATTGCTAATGTTTGTAATGAGGCAGCTTT
GATCGCTGCACGCGATTTGAATACATCTATCGTTCTAAAGCACTTTGAACAAGCTATTGA
ACGAGTTATTGCTGGCATGGAGAAAAAAACAAATGTTCTTGCTCCCGACGAAAAGAGAAC
TGTAGCATTTCACGAGTCAGGTCATGCTGTATGTGGTTGGTTTCTTGAACATTCTGATCC
GTTACTTAAAGTTTCTATTATTCCACGTGGAAAAGGTCTTGGGTATGCACAATATCTTCC
AAAGGATCAATATCTATTGTCCAAAGAGCAGCTCTACGATAGAATGTGTATGACACTTGG
TGGACGCGTTGCAGAAGAAATATTTTTTGGAAGAATCACTACAGGAGCTCAGGATGATTT
GAAAAAAGTTACCGAAAGTGCATACTCACAAATTGTGAGATTTGGTATGAATGAGAAAGT
AGGAAAAGTAAGTTTTGACATGTCGCAACCTGGTGATCCTATGTTTAGTAAGCCTTATTC
TGAACAAACGGCACAACTTATTGACGAAGAAGCTCGTGCAATGATAAATGAGGCTCATAA
AAGAACAACAGAGTTATTATTGAAACATAAAGATGATGTTCAAAAGGTAGCAGAGCGTTT
ATTGAAAAATGAAGTTCTCAGTCGTGATGATATGATAGAATTACTTGGCAAACGACCATT
TGCTGAAAAATCAACATATGAGGAGTTTGTAGAAGGTACTGGTTCATTTGAAGAAGATAC
AGCACTTCCATCGGGACTTTCAAGTTGGAATAAAGAGAGAGAGAAAAAAGAAGAAAGTGA
AAATGAAAAAAAAGATGAAAAACAAGAGAAATGA

>g6701.t5 Gene=g6701 Length=805
MAYRLITTTCNKQLERTLLSSIKSRHLSVNLKSKHDLAFITRNSDKPSILEIFLNELRIL
TSSDGPKDKFFKPPKSTSNSQPSSSESNENPPQKPTKPSTSSTNNSNNKSPPDWNLGMFS
PNPSAGPKNNSGSSQGRPIGGGDPNPEQNKMLFYGALGFAAVIIALTYFEMGYKEISWRD
FINNYLGRGVVERLEVINKKWVRVKLMPGNVSDGVLWFNIGSVDSFERNLENAQADLNIE
PANYIPVIYKSEIEAANLTGLLPTLLIIGFLIYMMRRSADMMGGGRGRKGGGLFGGVMQS
TARLINPNEIGVKFTDVAGCEEAKIEIMEFVNFLKNPQQYIDLGAKIPKGALLTGPPGTG
KTLLAKATAGEANVPFITVSGSEFLEMFVGVGPSRVRDMFAMARKQAPCILFIDEIDAVG
RKRGGKSFGGHSEQENTLNQLLVEMDGFNTTTNVVVLAATNRLDILDKALLRPGRFDRQI
FVPAPDIKGRASIFKVHLANLKTDLDKVELARKMAALTPGFTGADIANVCNEAALIAARD
LNTSIVLKHFEQAIERVIAGMEKKTNVLAPDEKRTVAFHESGHAVCGWFLEHSDPLLKVS
IIPRGKGLGYAQYLPKDQYLLSKEQLYDRMCMTLGGRVAEEIFFGRITTGAQDDLKKVTE
SAYSQIVRFGMNEKVGKVSFDMSQPGDPMFSKPYSEQTAQLIDEEARAMINEAHKRTTEL
LLKHKDDVQKVAERLLKNEVLSRDDMIELLGKRPFAEKSTYEEFVEGTGSFEEDTALPSG
LSSWNKEREKKEESENEKKDEKQEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g6701.t5 CDD cd00009 AAA 348 483 1.92738E-27
14 g6701.t5 Coils Coil Coil 781 805 -
12 g6701.t5 Gene3D G3DSA:3.40.1690.20 - 165 255 8.4E-31
10 g6701.t5 Gene3D G3DSA:3.40.50.300 - 300 485 1.6E-65
11 g6701.t5 Gene3D G3DSA:1.10.8.60 - 486 561 4.1E-27
13 g6701.t5 Gene3D G3DSA:1.20.58.760 - 562 760 1.2E-67
7 g6701.t5 Hamap MF_01458 ATP-dependent zinc metalloprotease FtsH [ftsH]. 1 774 32.485737
25 g6701.t5 MobiDBLite mobidb-lite consensus disorder prediction 65 109 -
28 g6701.t5 MobiDBLite mobidb-lite consensus disorder prediction 73 109 -
26 g6701.t5 MobiDBLite mobidb-lite consensus disorder prediction 766 805 -
27 g6701.t5 MobiDBLite mobidb-lite consensus disorder prediction 784 805 -
5 g6701.t5 PANTHER PTHR43655 ATP-DEPENDENT PROTEASE 150 800 0.0
6 g6701.t5 PANTHER PTHR43655:SF7 AFG3-LIKE PROTEIN 1 150 800 0.0
1 g6701.t5 Pfam PF06480 FtsH Extracellular 156 243 5.2E-9
2 g6701.t5 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 352 483 3.2E-43
3 g6701.t5 Pfam PF17862 AAA+ lid domain 514 551 9.0E-13
4 g6701.t5 Pfam PF01434 Peptidase family M41 567 748 4.8E-65
16 g6701.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 150 -
18 g6701.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 169 -
15 g6701.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 170 254 -
19 g6701.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 255 275 -
17 g6701.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 276 805 -
24 g6701.t5 ProSitePatterns PS00674 AAA-protein family signature. 454 472 -
23 g6701.t5 SMART SM00382 AAA_5 347 486 2.7E-23
9 g6701.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 311 557 2.77E-67
8 g6701.t5 SUPERFAMILY SSF140990 FtsH protease domain-like 567 758 2.88E-66
29 g6701.t5 TIGRFAM TIGR01241 FtsH_fam: ATP-dependent metallopeptidase HflB 258 750 7.0E-203
22 g6701.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 151 173 -
21 g6701.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 253 275 -

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:0016020 membrane CC
GO:0005524 ATP binding MF
GO:0004222 metalloendopeptidase activity MF
GO:0006508 proteolysis BP
GO:0008270 zinc ion binding MF
GO:0016021 integral component of membrane CC
GO:0004176 ATP-dependent peptidase activity MF
GO:0016887 ATP hydrolysis activity MF

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