Gene loci information

Transcript annotation

  • This transcript has been annotated as Peroxisomal biogenesis factor 6.

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_4 g16663 g16663.t1 TTS g16663.t1 10435118 10435118
chr_4 g16663 g16663.t1 isoform g16663.t1 10435258 10438989
chr_4 g16663 g16663.t1 exon g16663.t1.exon1 10435258 10435460
chr_4 g16663 g16663.t1 cds g16663.t1.CDS1 10435258 10435460
chr_4 g16663 g16663.t1 exon g16663.t1.exon2 10435596 10435781
chr_4 g16663 g16663.t1 cds g16663.t1.CDS2 10435596 10435781
chr_4 g16663 g16663.t1 TSS g16663.t1 10435882 10435882
chr_4 g16663 g16663.t1 exon g16663.t1.exon3 10436456 10438245
chr_4 g16663 g16663.t1 cds g16663.t1.CDS3 10436456 10438245
chr_4 g16663 g16663.t1 exon g16663.t1.exon4 10438325 10438989
chr_4 g16663 g16663.t1 cds g16663.t1.CDS4 10438325 10438989

Sequences

>g16663.t1 Gene=g16663 Length=2844
ATGCATTCGACCTCGATGTTACGGACATTACTCTATGTCTGCAAACTTCATTATCCAAAA
TATCCACCTTATTATTTTCCAGTTTACTTAATTGTAAAATTTCTTCAAGAATTCGACTTC
AAATTTAATACTCGAAAGTTAAATTTTCAACTTGTGCCGGTGCCAAATGAATATTTTGAC
TTTCTCTGTCGTGATCATGAAATTCAATCTGATCATACAATTTTCATCAATCGTCGAGTT
TTTGACTATTACATTTACCAAAAAGATGTCAATTTCATAAATTTACATCTTAGTGAATTC
AACAAACGAACAAATTTGACTCATGCAGAAAAAGTCATTAAAGAAGTTGTCGAGAGCACA
AAAGCAGCTGAATCCAACATGAACCTTTATCAAGTTTTTCCACTCAATATTCCGATCAAT
AAAATTTTCATGAAAGAAAATTCTTACTGGAATTTTGTTGACAAACATAAATTGATGGCC
ACAAATGAAGATTTAATTGTGAATTTGTCAATGTTGAAAGAAAATCAAAAAATTCCTGCA
ATTGCAACTAAATGCAATGTTTTTTTGATCAATTCACCTTATGAAGTACCAAATGCATTT
ATTGATGATGTGCTAAGAGAATACTTTAGGAAACCAAGATTGTTGTATAGAAATCACACT
TATAGAATTGACCTAACAGAAAAAGAACTAGGAAATTTCATCTTTTGTGACAATTTTTCA
CTAATTTCAAAGTTAAAACGTCTCTATTTCAAATGCGTTCATTTGGAATCACGCACAAAT
CTTTTTGACAATTGTGGAGTTGTTATAAATCAATTATCAACTTTAAATTTAACATCAACT
ATTAATTGTCGTCTACCAAGTGTCAATTTTTCATCGCATTATCAAACAATTCATCCTTAT
GGACTTGATTTAGTTTTCAATTCACTTAAATCTTCAATTCAGCCTTATTTAGAAGATGAA
AATTCAAAATTCTTAAAAAGCCGCAAAATATTTCCAATTTTCAATTTAGTAGGTGAACGC
GGAAGTGGAAAAACAAAAATTGTCCAATCTTTGGCTTCACATTTTGGACTACAAATTTAT
TTTGCTGAATGTTGTGAAATGATGACCGGAATGGCTTCAACAAGTGAACAAAAAATTCTT
TATACTCTTCATCGTGCTACAAACTGCAATCCTGTCATGTTGGTCATAAATGATTTTGAA
TATTTTGGACGCAATAATGAAGGTCATGAAGATGAAAGAATCATAAATTTTTTCAAAAAT
GAAGTTGTTAAAATTTTCAAATGTGAACTTCCAATTATTGTCATTGCCTTGAGTAATTGT
GAATTAAAAAATATTTTATCTGAAATTTTCTTAGAAACAATCACAATGAAACCATTAGAT
AAAAATGAAAGATTCAAATGTCTGCTTTGGCAACATCAACGTGAAATTTATGATCGACTT
TGTTATAAGATAAAAATTGGAAAACTTGACAATTACATAAATTATAAAATTCCAGAAGCA
ACAAAAGAAAATGATTTGAAAATTCTTAAATCAATGGCAGAACAAACTACAGGATTTATA
TTGGGTGACCTTAGAATTCTTTATCAAAGATCGATTCAAAATTTACGTGAATCAACACAA
AGTTCATCAGAATCATCTTTTTATTCACCAAATTTATCTTTAAATGAGGATGAATTTAAA
AAACAATTATCGATCATCAAAAAATGCTTCAGTGACAGCATTGGAACTCCAGAAATACCA
AAAGTCTTATGGGAAGATATTGGAGGTCTTGCAAACTTAAAAACTGAAATTCAAAACAGC
ATTGGTCTGCCATTGAAATATTCACATTTATTAGGAGGTAAAAATATGAAAAGATCAGGA
ATTTTACTCTTTGGTCCACCCGGAACTGGGAAAACTTTAATTGCAAAAGCTGTAGCAACT
GAATGCAATCTTAGCTTCATTTCTGTGCAAGGTCCAGAACTGCTTAATATGTATGTGGGT
CAATCTGAGCAAAATGTTCGTGAAGTTTTTAATAAAGCAAGAGCTTGTGCACCAGCAGTA
ATTTTTCTTGATGAACTTGATTCATTGGCACCAAATCGTGGTGTTGCCGGTGATTCTGGT
GGTGTTATGGATCGTGTTGTATCACAATTATTAAGTGAAATGGATGGAGTTGATGATGAT
CCAAAGAAACCAATTTTTGTGCTTGGAGCAACAAATCGACCTGATTTGATTGATAAACAA
TTATTGAGGCCAGGAAGGTTTGATAAAATGCTCTATGTTGGACCATGTCAAAGTGTTGAT
GATAAAGAATTGGTTTTAAAAGCATTGACAAGGAAATTTAATTTAAAAAAAGAAGTTAGT
GTGAGAAAAATTGCAGAACTTGTCAAATGTGATGTCACTGGTGCTGATTTGTATTCAATT
TGCTCAAATGCATGGTTGAGTGCTGTTAGAAAACAAGTCAAAGCTTTTGAAGCTGGAGAT
GCAAGACATATAACTGTAATGGAGGGCAATGACAGATTTTTCGTTGCAAGAAAGGAATAT
AATGGTGATCTTGTGATTGGAAAATTTAATTATGAGACAAACACAATTTATTTACCTTAT
CATGGTAAAGAAATTGCTATACAAACTATTGAAGTTGAACTTTTGAATCCTAACATAGAA
TTGAAATGGGTTCCATTTCCTGGCGGCATTCCAGAAAATGCCTATGAATTTGGTCGAGAA
AAAAATTTAAGAGTTTTTGTCGGAAAAGTATTACATGAAGAAAAAAATATTATTGGAAAA
GTCATTCCTGGTTTGAACAAACTATTTATTCCATACTACGGCCAAGAACTTTCTTTCAAC
AATTTTGAAATTCTTGTTTATTAA

>g16663.t1 Gene=g16663 Length=947
MHSTSMLRTLLYVCKLHYPKYPPYYFPVYLIVKFLQEFDFKFNTRKLNFQLVPVPNEYFD
FLCRDHEIQSDHTIFINRRVFDYYIYQKDVNFINLHLSEFNKRTNLTHAEKVIKEVVEST
KAAESNMNLYQVFPLNIPINKIFMKENSYWNFVDKHKLMATNEDLIVNLSMLKENQKIPA
IATKCNVFLINSPYEVPNAFIDDVLREYFRKPRLLYRNHTYRIDLTEKELGNFIFCDNFS
LISKLKRLYFKCVHLESRTNLFDNCGVVINQLSTLNLTSTINCRLPSVNFSSHYQTIHPY
GLDLVFNSLKSSIQPYLEDENSKFLKSRKIFPIFNLVGERGSGKTKIVQSLASHFGLQIY
FAECCEMMTGMASTSEQKILYTLHRATNCNPVMLVINDFEYFGRNNEGHEDERIINFFKN
EVVKIFKCELPIIVIALSNCELKNILSEIFLETITMKPLDKNERFKCLLWQHQREIYDRL
CYKIKIGKLDNYINYKIPEATKENDLKILKSMAEQTTGFILGDLRILYQRSIQNLRESTQ
SSSESSFYSPNLSLNEDEFKKQLSIIKKCFSDSIGTPEIPKVLWEDIGGLANLKTEIQNS
IGLPLKYSHLLGGKNMKRSGILLFGPPGTGKTLIAKAVATECNLSFISVQGPELLNMYVG
QSEQNVREVFNKARACAPAVIFLDELDSLAPNRGVAGDSGGVMDRVVSQLLSEMDGVDDD
PKKPIFVLGATNRPDLIDKQLLRPGRFDKMLYVGPCQSVDDKELVLKALTRKFNLKKEVS
VRKIAELVKCDVTGADLYSICSNAWLSAVRKQVKAFEAGDARHITVMEGNDRFFVARKEY
NGDLVIGKFNYETNTIYLPYHGKEIAIQTIEVELLNPNIELKWVPFPGGIPENAYEFGRE
KNLRVFVGKVLHEEKNIIGKVIPGLNKLFIPYYGQELSFNNFEILVY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g16663.t1 CDD cd00009 AAA 617 755 0e+00
11 g16663.t1 Gene3D G3DSA:3.40.50.300 - 289 473 0e+00
12 g16663.t1 Gene3D G3DSA:3.40.50.300 - 580 755 0e+00
13 g16663.t1 Gene3D G3DSA:1.10.8.60 - 757 818 0e+00
4 g16663.t1 PANTHER PTHR23077:SF9 PEROXISOME ASSEMBLY FACTOR 2 191 823 0e+00
5 g16663.t1 PANTHER PTHR23077 AAA-FAMILY ATPASE 191 823 0e+00
3 g16663.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 336 440 1e-07
2 g16663.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 621 754 0e+00
1 g16663.t1 Pfam PF11901 Protein of unknown function (DUF3421) 830 938 0e+00
9 g16663.t1 SMART SM00382 AAA_5 330 460 2e+01
8 g16663.t1 SMART SM00382 AAA_5 617 757 0e+00
10 g16663.t1 SMART SM00696 dm9 880 947 2e-07
7 g16663.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 329 535 0e+00
6 g16663.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 580 824 0e+00

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:0005524 ATP binding 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