Gene loci information

Transcript annotation

  • This transcript has been annotated as Peroxisome biogenesis factor 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_3 g780 g780.t1 TSS g780.t1 5979885 5979885
chr_3 g780 g780.t1 isoform g780.t1 5979999 5983733
chr_3 g780 g780.t1 exon g780.t1.exon1 5979999 5980052
chr_3 g780 g780.t1 cds g780.t1.CDS1 5979999 5980052
chr_3 g780 g780.t1 exon g780.t1.exon2 5980108 5980203
chr_3 g780 g780.t1 cds g780.t1.CDS2 5980108 5980203
chr_3 g780 g780.t1 exon g780.t1.exon3 5980284 5980590
chr_3 g780 g780.t1 cds g780.t1.CDS3 5980284 5980590
chr_3 g780 g780.t1 exon g780.t1.exon4 5980669 5983733
chr_3 g780 g780.t1 cds g780.t1.CDS4 5980669 5983733
chr_3 g780 g780.t1 TTS g780.t1 NA NA

Sequences

>g780.t1 Gene=g780 Length=3522
ATGTTTGCGAGAAATTTTGCAGTGAAATATAAACCAATCAAATCAAATTTTGTGTTACTT
CCAGAAAACTATAGAAGACTTGTATCAACATGTAAAACAGGCTGTCTCTTGTTACATTTC
CTTGATTATCGATCAAATCAGTATAAGACGGTATATGTGTCATGGTCAGCAACAATTCAG
GCAAATAATCCGTTTGAAGAAGAGGAAATTGGCATTAACGCTCAGTTAGCTGAACTATTT
GGCTTAAAAGAAGGCGTCAATGTATCATGTTCTGTCATTCAAAATGCCTCTCCAGTTCGT
TCAATGTCAATTTCGCTCTCTGATGAAGACTATCAAGTAGCAGAATGTTCACTCGATCGT
TTACAATACGATATGTTAGATCAAGTTTCAATTGTTGGCCGTTATCAGCCAATAATTATC
TGGTTAAATAAATCGATAGCCGTCAACGCAACCGTGGACAACTTAAGTCCAACTTTCAAC
TACGGTCGTATATTAAATGACACTGAAATATCAATAAATCGGAAAATGACCCCTGACTTT
CTTCGGAGGAAGCCGAAGAATGCGACAACAGACGATTCGTCAGAATCAAAAATAACAAAA
CGTATGAGTGCGATTGAAAAATCAGAAACAGTCGACTTATCAAACATGCCACATCTAAGG
CGCAATAACAGTTTTATAGATTCAAGAAAATTTTTGGATACTTCAGAAACAAATGGCTTT
GGCCGGAGAACTTCAACATCAAATAATTCTAATGGAGGTTGGTCAGACACTATTTATAGT
GACGTAACATCAAAAAAACCACCAACTGCGAGTCCAAGAAGTAGCATTAAAAAAATTAAA
GATAATAGTGAAAATGGAAAAAATTTAACTAATGGTGAATCGTTACTTAAACGAAATTCA
ATTACTTCAAGTGCAAGTTTAAGTAATATTAAAGCATTTAATGAAAATAATGGTAGAGCA
GAGAGTAAAGAAAGAGAATTTGTACCAATATCCAATAGCTTAAGTACAAGTAATATAAAA
CGAGTTCAAGAGAAGTCGAATAAATTTCTCGAGCAGTTATCAAATCAAGAATCGCCTGCA
AGAAAATTGTTAAATAGTGCGAGTGCAAGTTGTTTGCCAAAAGTTCTCGTGTCACCAACA
TCACCGACTGAGACTAAACAAAATCACAAATTACTTTTGGAAGATATGAAGAAAGCACTT
TTTCGTGAGACACATAAAAGACATTTTATGAAGATAAAAATTGTGAGTGATAAGAAAAAA
TTGGATAAGTTTATGCAAATCAACGATATTTATATTTCAAAAAATGCATCCTCATGTATA
AATATTAACCAAATTCATAAAGTACGTACCAAAGAAGAGAAAGAGTATCATGTTCGTATA
AAATGTAATGAATCATTGCCCTTTGATACAATTGAAGTTCATCCTGTTCTTGCCAAAGTA
CTTAATATCGAACAAGGTTTTCGAGTTGAATTGTCAGAGACTAAGCTTGTTTGTAATTGC
ATTGAAAGTCTTGAAATAATTCCGTACTCAAACATTTCGGAAAATAATTTTGGTCTACAA
ATAGCAAAAGATATTGATGAAAAATTTAAAAAATATGTAAATGCCAATACGAAATTAGTT
CCATTAATTCTTAATCAAAATCAAATTTTTAAACTTGATGATTATTTGTTGACAATAAAA
ATATTTCCACTCTCAACGCATGCATGCTGTATTGACAGTGAAATACTTCGTGAAGGAATT
ATTGATGTTATGAAAAGAGGCGAACCACATGAATTTGCCAATTTATTACGAGACGAAAAT
GAAAGACGAAATAAAAAAACGGAAATAGAAAAAATTGTCAAGTTAGATAAACATCAACAG
ATTGTAGATCGTTTCACAAATGAAATTCATTCAACTACAAATGATTATCGTGTAATGAAT
GTGGATCAAAACAACAGCATTATTTCTGGTGCAACACACTCGGGAAAGAAAACAATTTGC
AACGAAATAAAAAAGAATTTGGAAGCACGAAATGTAAATGTAATAGTTTTTAACTGCGCA
CAATATAAAGGAAGAAAAGTTGAGTCGATTGTTAAGGATATGAAAATAATGATGAAAGAG
TGTCTTCAAACTGCACCGTCCACTTATATAATTCATAATTTAGACGCTCTGTGCACGCAA
TCACATGATGACGAACAACAATCACAAGAAAACGAATATCAACAGAAATTGGCAAACAAC
ATACGACACGTGTTCGAAGAATTCACACACGACTATGGAAATATGATTTCAATCGTCGTC
ACCACATCAAAAATGTCAAACTTGAGTAAAAACATTTTTCGTAGTTATGGTAATTATCTA
TTTAAAAATGTTGTGAAAATTCCCAACCTCGAGGCGTTCGATCGACGTGAGTTGTTTAAA
AATTTCTTTCATACATCTTCGCATGTGAAAATTGATTCTTCACTCGATTGGGACAAATTT
GCGAGAATCACTGAGGGATACAATATTGGCGACATTTGCCAATTTACAGATCGAGCAATT
TTCTTCGCTATAAAAGAAAATTACAAAAGTCCACTATTGACCGAAGATATTTTACGAAAA
TCTTTAAATGTTTCAAACAAATTGTGTCTTGAGGGAATAAAAACTGAATCAATTGATAGT
GACGATGCACAAATTGATATAAAAGAGGAAATTCCTGGTATGGATAATGTTATCGAAACA
CTTGAAGAAGTCTTAATATGGCCAACAAAGTTTTCAAAAATATTTCAAAATTCACCATTG
AGAAATCAAGCGGGCATTCTGTTATTTGGTTTTCCAGGTTCGGGAAAAAATTTTATTGTC
TCACAAATAACAAAACGATGGAATTTAAGATTAATATCAATTAAAGGACCAGAACTATTG
GCAAAATATATTGGTCAAAGTGAAGAGAATGTGAGAAATTTGTTTGAGAAAGCAAAATCA
GCCAAACCATGTGTTCTCTTCTTTGATGAATTTGAGAGTTTAGCACCACGAAGGGGTCAC
GACTCGACTGGCGTTACTGACAGAGTCGTTAATCAACTGTTAACAGAATTGGATGGTGTA
AAAAGTTTAGAAGGAGTTTCAATTATATGTGCTACCTCTAGACCCGATCTTATCGATCCT
GCATTATTACGTAGTGGAAGAATTGATCGTTTGGTTGAATGTCAATTGCCAAATGCATCC
GAAAGATTGGATATTTTGAAATATTTATCTAAATCTTTATTAATAGACTCAAATGTGGAC
TTTAAAGTTCTAGCATCAAAAATGACTACATTCACTGGAGCTGATATTAAAAGTGTACTA
ACAACAGCAAATATGAATGCTATCGAAGAAGAAATAAAGAAAAATAATGGAAGAGCGATA
GAAAATGTTGAAATTAAGCAAACTCATTTAGAAGCAGCTTTTCAAAATACTCGTGCTTCT
TTAACTAAACAGGATATTGAAAAATATCAAATGCTTTATGATAGATTCAAAAACAAAAAG
TCTGTAACAGTTGAAACACCACAACGTGTTAGTTTAGCATAA

>g780.t1 Gene=g780 Length=1173
MFARNFAVKYKPIKSNFVLLPENYRRLVSTCKTGCLLLHFLDYRSNQYKTVYVSWSATIQ
ANNPFEEEEIGINAQLAELFGLKEGVNVSCSVIQNASPVRSMSISLSDEDYQVAECSLDR
LQYDMLDQVSIVGRYQPIIIWLNKSIAVNATVDNLSPTFNYGRILNDTEISINRKMTPDF
LRRKPKNATTDDSSESKITKRMSAIEKSETVDLSNMPHLRRNNSFIDSRKFLDTSETNGF
GRRTSTSNNSNGGWSDTIYSDVTSKKPPTASPRSSIKKIKDNSENGKNLTNGESLLKRNS
ITSSASLSNIKAFNENNGRAESKEREFVPISNSLSTSNIKRVQEKSNKFLEQLSNQESPA
RKLLNSASASCLPKVLVSPTSPTETKQNHKLLLEDMKKALFRETHKRHFMKIKIVSDKKK
LDKFMQINDIYISKNASSCININQIHKVRTKEEKEYHVRIKCNESLPFDTIEVHPVLAKV
LNIEQGFRVELSETKLVCNCIESLEIIPYSNISENNFGLQIAKDIDEKFKKYVNANTKLV
PLILNQNQIFKLDDYLLTIKIFPLSTHACCIDSEILREGIIDVMKRGEPHEFANLLRDEN
ERRNKKTEIEKIVKLDKHQQIVDRFTNEIHSTTNDYRVMNVDQNNSIISGATHSGKKTIC
NEIKKNLEARNVNVIVFNCAQYKGRKVESIVKDMKIMMKECLQTAPSTYIIHNLDALCTQ
SHDDEQQSQENEYQQKLANNIRHVFEEFTHDYGNMISIVVTTSKMSNLSKNIFRSYGNYL
FKNVVKIPNLEAFDRRELFKNFFHTSSHVKIDSSLDWDKFARITEGYNIGDICQFTDRAI
FFAIKENYKSPLLTEDILRKSLNVSNKLCLEGIKTESIDSDDAQIDIKEEIPGMDNVIET
LEEVLIWPTKFSKIFQNSPLRNQAGILLFGFPGSGKNFIVSQITKRWNLRLISIKGPELL
AKYIGQSEENVRNLFEKAKSAKPCVLFFDEFESLAPRRGHDSTGVTDRVVNQLLTELDGV
KSLEGVSIICATSRPDLIDPALLRSGRIDRLVECQLPNASERLDILKYLSKSLLIDSNVD
FKVLASKMTTFTGADIKSVLTTANMNAIEEEIKKNNGRAIENVEIKQTHLEAAFQNTRAS
LTKQDIEKYQMLYDRFKNKKSVTVETPQRVSLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g780.t1 CDD cd00009 AAA 647 775 0.00864505
15 g780.t1 CDD cd00009 AAA 892 1056 1.27322E-21
13 g780.t1 Gene3D G3DSA:3.10.330.10 - 101 176 1.8E-11
11 g780.t1 Gene3D G3DSA:3.40.50.300 - 602 806 2.1E-10
12 g780.t1 Gene3D G3DSA:3.40.50.300 - 888 1056 7.0E-53
14 g780.t1 Gene3D G3DSA:1.10.8.60 - 1057 1158 1.4E-19
20 g780.t1 MobiDBLite mobidb-lite consensus disorder prediction 259 297 -
5 g780.t1 PANTHER PTHR23077 AAA-FAMILY ATPASE 53 1156 9.4E-140
6 g780.t1 PANTHER PTHR23077:SF12 PEROXISOME BIOGENESIS FACTOR 1 53 1156 9.4E-140
3 g780.t1 Pfam PF09262 Peroxisome biogenesis factor 1, N-terminal 106 172 4.3E-10
2 g780.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 648 774 6.4E-6
1 g780.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 926 1054 5.3E-37
4 g780.t1 Pfam PF17862 AAA+ lid domain 1078 1115 2.5E-6
17 g780.t1 ProSitePatterns PS00674 AAA-protein family signature. 1026 1044 -
18 g780.t1 SMART SM00382 AAA_5 642 803 0.9
19 g780.t1 SMART SM00382 AAA_5 922 1058 5.7E-11
7 g780.t1 SUPERFAMILY SSF50692 ADC-like 6 94 1.44E-8
10 g780.t1 SUPERFAMILY SSF54585 Cdc48 domain 2-like 106 172 2.88E-10
8 g780.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 642 864 1.43E-15
9 g780.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 889 1156 7.44E-54

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:0007031 peroxisome organization BP
GO:0005524 ATP binding MF
GO:0006625 protein targeting to peroxisome BP
GO:0005777 peroxisome CC
GO:0016887 ATP hydrolysis activity MF
GO:0005778 peroxisomal membrane CC

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