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.t11 TSS g6701.t11 18110476 18110476
chr_2 g6701 g6701.t11 isoform g6701.t11 18111237 18113220
chr_2 g6701 g6701.t11 exon g6701.t11.exon1 18111237 18111622
chr_2 g6701 g6701.t11 cds g6701.t11.CDS1 18111297 18111622
chr_2 g6701 g6701.t11 exon g6701.t11.exon2 18111683 18111816
chr_2 g6701 g6701.t11 cds g6701.t11.CDS2 18111683 18111816
chr_2 g6701 g6701.t11 exon g6701.t11.exon3 18111881 18113220
chr_2 g6701 g6701.t11 cds g6701.t11.CDS3 18111881 18113220
chr_2 g6701 g6701.t11 TTS g6701.t11 18113191 18113191

Sequences

>g6701.t11 Gene=g6701 Length=1860
GGTCGTGGTGTTGTAGAGCGATTAGAAGTCATCAACAAAAAATGGGTTCGAGTTAAATTA
ATGCCTGGAAATGTTAGTGATGGTGTATTATGGTTTAATATTGGTAGCGTGGATTCTTTC
GAACGAAATTTAGAGAATGCACAAGCTGATCTCAATATAGAACCGGCAAATTATATTCCA
GTTATATATAAATCTGAAATTGAAGCCGCTAATTTAACAGGGCTTTTGCCGACTCTTCTC
ATTATTGGTTTCTTAATATATATGATGCGTCGTTCCGCTGATATGATGGGTGGAGGAAGA
GGCAGAAAAGGAGGTGGTCTTTTCGGCGGAGTAATGCAATCAACTGCAAGATTAATTAAT
CCTAATGAAATCGGAGTCAAATTTACTGATGTTGCTGGATGTGAAGAAGCTAAGATTGAG
ATCATGGAATTTGTAAATTTTTTGAAAAATCCTCAACAATACATTGACTTGGGTGCAAAA
ATTCCAAAAGGTGCTTTGTTAACCGGACCACCTGGCACAGGTAAAACTTTGTTGGCAAAA
GCAACTGCAGGCGAGGCAAATGTTCCATTCATCACTGTTTCTGGTAGTGAATTTTTAGAA
ATGTTTGTCGGTGTCGGTCCATCACGAGTTCGTGATATGTTTGCTATGGCACGAAAGCAA
GCTCCATGTATACTTTTTATTGATGAGATTGATGCAGTTGGTAGAAAGCGTGGTGGCAAA
TCATTCGGAGGTCACTCAGAACAAGAAAACACGTTAAATCAGCTTTTAGTAGAGATGGAT
GGATTTAATACAACAACAAATGTCGTTGTTTTAGCTGCTACAAATCGCTTAGACATATTA
GATAAGGCATTGCTTAGACCAGGCAGATTCGATCGTCAAATATTTGTTCCTGCGCCTGAT
ATCAAAGGTCGTGCATCAATTTTCAAAGTACATTTGGCTAATCTTAAAACAGATTTAGAT
AAAGTTGAACTTGCACGAAAAATGGCTGCATTAACTCCTGGTTTCACTGGTGCTGATATT
GCTAATGTTTGTAATGAGGCAGCTTTGATCGCTGCACGCGATTTGAATACATCTATCGTT
CTAAAGCACTTTGAACAAGCTATTGAACGAGTTATTGCTGGCATGGAGAAAAAAACAAAT
GTTCTTGCTCCCGACGAAAAGAGAACTGTAGCATTTCACGAGTCAGGTCATGCTGTATGT
GGTTGGTTTCTTGAACATTCTGATCCGTTACTTAAAGTTTCTATTATTCCACGTGGAAAA
GGTCTTGGGTATGCACAATATCTTCCAAAGGATCAATATCTATTGTCCAAAGAGCAGCTC
TACGATAGAATGTGTATGACACTTGGTGGACGCGTTGCAGAAGAAATATTTTTTGGAAGA
ATCACTACAGGAGCTCAGGATGATTTGAAAAAAGTTACCGAAAGTGCATACTCACAAATT
GTGAGATTTGGTATGAATGAGAAAGTAGGAAAAGTAAGTTTTGACATGTCGCAACCTGGT
GATCCTATGTTTAGTAAGCCTTATTCTGAACAAACGGCACAACTTATTGACGAAGAAGCT
CGTGCAATGATAAATGAGGCTCATAAAAGAACAACAGAGTTATTATTGAAACATAAAGAT
GATGTTCAAAAGGTAGCAGAGCGTTTATTGAAAAATGAAGTTCTCAGTCGTGATGATATG
ATAGAATTACTTGGCAAACGACCATTTGCTGAAAAATCAACATATGAGGAGTTTGTAGAA
GGTACTGGTTCATTTGAAGAAGATACAGCACTTCCATCGGGACTTTCAAGTTGGAATAAA
GAGAGAGAGAAAAAAGAAGAAAGTGAAAATGAAAAAAAAGATGAAAAACAAGAGAAATGA

>g6701.t11 Gene=g6701 Length=599
MPGNVSDGVLWFNIGSVDSFERNLENAQADLNIEPANYIPVIYKSEIEAANLTGLLPTLL
IIGFLIYMMRRSADMMGGGRGRKGGGLFGGVMQSTARLINPNEIGVKFTDVAGCEEAKIE
IMEFVNFLKNPQQYIDLGAKIPKGALLTGPPGTGKTLLAKATAGEANVPFITVSGSEFLE
MFVGVGPSRVRDMFAMARKQAPCILFIDEIDAVGRKRGGKSFGGHSEQENTLNQLLVEMD
GFNTTTNVVVLAATNRLDILDKALLRPGRFDRQIFVPAPDIKGRASIFKVHLANLKTDLD
KVELARKMAALTPGFTGADIANVCNEAALIAARDLNTSIVLKHFEQAIERVIAGMEKKTN
VLAPDEKRTVAFHESGHAVCGWFLEHSDPLLKVSIIPRGKGLGYAQYLPKDQYLLSKEQL
YDRMCMTLGGRVAEEIFFGRITTGAQDDLKKVTESAYSQIVRFGMNEKVGKVSFDMSQPG
DPMFSKPYSEQTAQLIDEEARAMINEAHKRTTELLLKHKDDVQKVAERLLKNEVLSRDDM
IELLGKRPFAEKSTYEEFVEGTGSFEEDTALPSGLSSWNKEREKKEESENEKKDEKQEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6701.t11 CDD cd00009 AAA 142 277 3.59022E-27
13 g6701.t11 Coils Coil Coil 575 599 -
11 g6701.t11 Gene3D G3DSA:3.40.1690.20 - 2 49 1.2E-13
9 g6701.t11 Gene3D G3DSA:3.40.50.300 - 94 279 9.5E-66
10 g6701.t11 Gene3D G3DSA:1.10.8.60 - 280 355 2.7E-27
12 g6701.t11 Gene3D G3DSA:1.20.58.760 - 356 554 7.0E-68
6 g6701.t11 Hamap MF_01458 ATP-dependent zinc metalloprotease FtsH [ftsH]. 1 568 31.892164
21 g6701.t11 MobiDBLite mobidb-lite consensus disorder prediction 560 599 -
22 g6701.t11 MobiDBLite mobidb-lite consensus disorder prediction 578 599 -
4 g6701.t11 PANTHER PTHR43655 ATP-DEPENDENT PROTEASE 3 594 0.0
5 g6701.t11 PANTHER PTHR43655:SF7 AFG3-LIKE PROTEIN 1 3 594 0.0
1 g6701.t11 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 146 277 2.0E-43
2 g6701.t11 Pfam PF17862 AAA+ lid domain 308 345 6.3E-13
3 g6701.t11 Pfam PF01434 Peptidase family M41 361 542 2.8E-65
15 g6701.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 48 -
16 g6701.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 68 -
14 g6701.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 69 599 -
20 g6701.t11 ProSitePatterns PS00674 AAA-protein family signature. 248 266 -
19 g6701.t11 SMART SM00382 AAA_5 141 280 2.7E-23
8 g6701.t11 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 105 351 1.51E-67
7 g6701.t11 SUPERFAMILY SSF140990 FtsH protease domain-like 361 552 1.7E-66
23 g6701.t11 TIGRFAM TIGR01241 FtsH_fam: ATP-dependent metallopeptidase HflB 52 544 2.8E-203
18 g6701.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 47 69 -

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:0006508 proteolysis BP
GO:0005524 ATP binding MF
GO:0004222 metalloendopeptidase activity MF
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