Gene loci information

Transcript annotation

  • This transcript has been annotated as Porphobilinogen deaminase.

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 g3336 g3336.t1 TTS g3336.t1 24727937 24727937
chr_3 g3336 g3336.t1 isoform g3336.t1 24728109 24729834
chr_3 g3336 g3336.t1 exon g3336.t1.exon1 24728109 24729523
chr_3 g3336 g3336.t1 cds g3336.t1.CDS1 24728109 24729523
chr_3 g3336 g3336.t1 exon g3336.t1.exon2 24729595 24729667
chr_3 g3336 g3336.t1 cds g3336.t1.CDS2 24729595 24729667
chr_3 g3336 g3336.t1 exon g3336.t1.exon3 24729775 24729834
chr_3 g3336 g3336.t1 cds g3336.t1.CDS3 24729775 24729834
chr_3 g3336 g3336.t1 TSS g3336.t1 24730033 24730033

Sequences

>g3336.t1 Gene=g3336 Length=1548
ATGACAACAAAACAAGATGATTTTCGTGAAATAATTAAAGTTGGCTCGAGAAAGAGTGAG
CTCGCTCTCATTCAAACAAAATATGTTATATCTCTTCTCTCTAAACTCTTTCCGAATGTC
AAGTTTGAAATTCATACTATGACAACGCTCGGTGATCGTGTACTTGGCATCTCGTTGCCA
AAAATTGGAGAAAAGTCTCTCTTTACTAAAGATTTAGAAGATGCACTTGAGCATGGTGGC
GTTGATTTTGTTGTCCATTCTCTCAAAGATTTGCCGACTCAATTGCCTTTTGGTATGGCT
GTTGGTGCAATTTTAGAGAGAGAAGATCCGCGAGATGCTTTGGTTCTTAACAATAAATTT
ATTGGGAAAAATTTGAAGTCACTGCCAAAGGGATCTCTTATCGGAACATCGAGTCTTAGA
CGTTGCGCTCAACTTGCACGACATTATAATCATCTCAAGATTTGTGACATTCGTGGAAAT
TTAAATACTCGCTTGGCAAAATTAGATGCACCACAATCGAAATTTGCGGGAATTATTTTG
GCTCATGCTGGTCTTTGTCGTATGGGATGGATGAAAAGAGTCGATCAAGTGATTGAGCCT
GAAGAATTGTTATATGCTGTTGGACAAGGAGCTTTGGCTGTTGAATGTCGTGCAAATGAT
ACATTTGTTTTGGACATTTTATCAAAGCTTTGTGATGTCAAAACTCAATGCCGAATTTTG
GTTGAAAGAAGTTTCCTCAAGACTCTTGGTGGTGGTTGTTCTGCTCCAGTTGCCATAAAC
TCTGTATTAAGTGAAATTCCAAATTCTGTTAATGAAGAATATGTGATGGATGTTGAAGGT
GCTGTGTGGTCATTAAATGGCGATACTGAGATTAAAGATAAAATTTCGTTAAATTTGGTT
TTCAAAAATGCTGATACAAAAGCAAGTGATGTTCCAAATAAGCGTCAAAAGATGAGTGAA
GGGAATATAAGCCCTGAAGTGATTGATGAAAATCCTTTTAAAGGAGATATTGAAGACCTT
GTTAATATTCATGGAAAGGTTTGTCCATCGACAAAGAAAAATTGTACTGGTGTTTGTGAT
TCGAAGGATAAGAAAAAGTTTGATCCATCGATAATTCCAGTTGGACAAGATTTTATGGGT
GAATGTCCAGTTTTAAATACAGCTCAGAAAGTTTCATTTTCAATTGATTGCGATCAAAAA
GGCGATTCACCTTGCACTGCCTGTCCTTTTGTTCAGAAATCTCCGGAAGAAATTCCAAAA
GAAGCAATTGAAAAATGCCCTTTCTTCCAACAACAAAAATCTAATAAACCAGTTCAAATG
ATTGATTATGAAGAAAATGCGAAACATGATACAACTGAAAAGAAATCTCTGATTGCCGGC
ATGAAAGAGATTAAGCTCTATTGCGGGCTTTTCTGTCATTCCGAACGTACTCGTGAGTTG
TTTGAAAAATGTGAAAATCTCGGCATCGAGTTGGCAAATAAATTGATTGCAGCTAACGCT
TTGGAAGTGATGAAAATTGCTCAAGACGAAATTCATTCAAAAGCTTAA

>g3336.t1 Gene=g3336 Length=515
MTTKQDDFREIIKVGSRKSELALIQTKYVISLLSKLFPNVKFEIHTMTTLGDRVLGISLP
KIGEKSLFTKDLEDALEHGGVDFVVHSLKDLPTQLPFGMAVGAILEREDPRDALVLNNKF
IGKNLKSLPKGSLIGTSSLRRCAQLARHYNHLKICDIRGNLNTRLAKLDAPQSKFAGIIL
AHAGLCRMGWMKRVDQVIEPEELLYAVGQGALAVECRANDTFVLDILSKLCDVKTQCRIL
VERSFLKTLGGGCSAPVAINSVLSEIPNSVNEEYVMDVEGAVWSLNGDTEIKDKISLNLV
FKNADTKASDVPNKRQKMSEGNISPEVIDENPFKGDIEDLVNIHGKVCPSTKKNCTGVCD
SKDKKKFDPSIIPVGQDFMGECPVLNTAQKVSFSIDCDQKGDSPCTACPFVQKSPEEIPK
EAIEKCPFFQQQKSNKPVQMIDYEENAKHDTTEKKSLIAGMKEIKLYCGLFCHSERTREL
FEKCENLGIELANKLIAANALEVMKIAQDEIHSKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g3336.t1 CDD cd13645 PBP2_HuPBGD_like 12 296 1.39638E-149
13 g3336.t1 Gene3D G3DSA:3.40.190.10 - 12 221 1.1E-78
12 g3336.t1 Gene3D G3DSA:3.40.190.10 - 109 213 1.1E-78
14 g3336.t1 Gene3D G3DSA:3.30.160.40 Porphobilinogen deaminase (hydroxymethylbilane synthase) 232 335 1.8E-17
3 g3336.t1 PANTHER PTHR11557:SF0 PORPHOBILINOGEN DEAMINASE 4 509 1.7E-121
4 g3336.t1 PANTHER PTHR11557 PORPHOBILINOGEN DEAMINASE 4 509 1.7E-121
5 g3336.t1 PRINTS PR00151 Porphobilinogen deaminase signature 51 71 4.8E-38
7 g3336.t1 PRINTS PR00151 Porphobilinogen deaminase signature 82 101 4.8E-38
6 g3336.t1 PRINTS PR00151 Porphobilinogen deaminase signature 133 150 4.8E-38
9 g3336.t1 PRINTS PR00151 Porphobilinogen deaminase signature 152 169 4.8E-38
8 g3336.t1 PRINTS PR00151 Porphobilinogen deaminase signature 241 258 4.8E-38
2 g3336.t1 Pfam PF01379 Porphobilinogen deaminase, dipyromethane cofactor binding domain 12 223 4.0E-75
1 g3336.t1 Pfam PF03900 Porphobilinogen deaminase, C-terminal domain 238 299 2.2E-8
16 g3336.t1 ProSitePatterns PS00533 Porphobilinogen deaminase cofactor-binding site. 242 258 -
11 g3336.t1 SUPERFAMILY SSF53850 Periplasmic binding protein-like II 11 229 6.3E-72
10 g3336.t1 SUPERFAMILY SSF54782 Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 232 298 6.02E-9
17 g3336.t1 TIGRFAM TIGR00212 hemC: hydroxymethylbilane synthase 12 266 3.0E-87

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:0018160 peptidyl-pyrromethane cofactor linkage BP
GO:0033014 tetrapyrrole biosynthetic process BP
GO:0004418 hydroxymethylbilane synthase 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