Gene loci information

Transcript annotation

  • This transcript has been annotated as Uroporphyrinogen decarboxylase.

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_1 g14174 g14174.t11 TSS g14174.t11 35236699 35236699
chr_1 g14174 g14174.t11 isoform g14174.t11 35236794 35238164
chr_1 g14174 g14174.t11 exon g14174.t11.exon1 35236794 35236811
chr_1 g14174 g14174.t11 exon g14174.t11.exon2 35236979 35238164
chr_1 g14174 g14174.t11 cds g14174.t11.CDS1 35237059 35238042
chr_1 g14174 g14174.t11 TTS g14174.t11 35238155 35238155

Sequences

>g14174.t11 Gene=g14174 Length=1204
ATGCAATATCAACCGAAGAGAACTTTCCTGTGCTCAAAAATGACAATCTATTGCGTGCGG
CTCGTGGTGATAAAGTTGATCGAGTGCCGGTTTGGGTGATGAGACAAGCTGGAAGATATC
TACCTGAATTTCGTGAAGTTCGCGCTGAAAGTGATTTCTTCAAAGTCTGTCGTACACCTG
AACTTGCTGTTGAAGTCACTATGCAACCTATTCGACGATTCGATCTTGATGCATCGATTA
TCTTTTCTGATATTCTCGTCATTCCACAAGCTCTTGGTATGGAAGTTGAAATGAGACCAG
GTCACGGACCGGTTTTTCCTGAGCCATTGCAAGATATTAAAGATGTGTCACGATTGAATG
CTGATGGCGCTATCGATAGATTAAAATACGTTGGTGATGCAATTACACTCATGAGACATA
CACTCGAAGGAAAAGTTCCACTCTTTGGATTTACTGGTGCTCCATGGACACTTATGGGTT
ACATGATTGAAGGAGGTGGCAGCAAAACAATGTCAAAGGCTCGTAGTTGGCTTAAAGATC
ATTCCGAAGAATCTCGCAATCTTCTTTCTCTTCTCACTGATGTTATTGTTGATTATTTAG
TGATGCAAGTGAAAGCTGGTGCACAAATTTTACAAGTGTTCGAATCAAGTGCTGAATATA
TCAGCAAAGAAGAATTTATTGAATTTGCACTGCCATACCTAAAAGAAATTCGAATTAAAA
CACAAGAGAAACTCAATAAACAAGACATTGAGCTCGTTCCAATGGTTGTATTTGCAAAAG
GTGCCATGCATTCACTAGCTGAAATGTCTGATTTGGGATACGATGTCATCGGACTTGACT
GGACAGTTGATCCTGAAGAAGCAAGAAAAATTGTTGGACCAAATGTCACACTTCAAGGAA
ATTTGAATCCACAAGATCTTTATAAATCGCAAGAGGAAATTCGTGAATTGACAAGAACTA
TGGTGAGAAAGTTTGGAAAAGATCGTTACATTGCTAATCTTGGACATGGAATTACGCCTC
AAACACCAATTGAGAGCATGACAACTTTTGTTGATACCGTTCATTCCGCTTTTGACGATT
AAAAATCGACATTGCATTTTATACTCTCTAAATAACTCTTTATGTTGTGTTTAAACTATG
TTTTTAAAACGGGTGATCAAATTTTTTGAATAAATTTGATAATTTTTATTAAAAGACAAA
TGAA

>g14174.t11 Gene=g14174 Length=327
MRQAGRYLPEFREVRAESDFFKVCRTPELAVEVTMQPIRRFDLDASIIFSDILVIPQALG
MEVEMRPGHGPVFPEPLQDIKDVSRLNADGAIDRLKYVGDAITLMRHTLEGKVPLFGFTG
APWTLMGYMIEGGGSKTMSKARSWLKDHSEESRNLLSLLTDVIVDYLVMQVKAGAQILQV
FESSAEYISKEEFIEFALPYLKEIRIKTQEKLNKQDIELVPMVVFAKGAMHSLAEMSDLG
YDVIGLDWTVDPEEARKIVGPNVTLQGNLNPQDLYKSQEEIRELTRTMVRKFGKDRYIAN
LGHGITPQTPIESMTTFVDTVHSAFDD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g14174.t11 CDD cd00717 URO-D 1 323 1.39618E-173
6 g14174.t11 Gene3D G3DSA:3.20.20.210 - 1 326 2.6E-142
2 g14174.t11 PANTHER PTHR21091:SF169 UROPORPHYRINOGEN DECARBOXYLASE 1 323 1.6E-159
3 g14174.t11 PANTHER PTHR21091 METHYLTETRAHYDROFOLATE:HOMOCYSTEINE METHYLTRANSFERASE RELATED 1 323 1.6E-159
1 g14174.t11 Pfam PF01208 Uroporphyrinogen decarboxylase (URO-D) 1 323 1.7E-118
5 g14174.t11 ProSitePatterns PS00907 Uroporphyrinogen decarboxylase signature 2. 116 132 -
4 g14174.t11 SUPERFAMILY SSF51726 UROD/MetE-like 1 323 6.8E-101
7 g14174.t11 TIGRFAM TIGR01464 hemE: uroporphyrinogen decarboxylase 1 323 4.9E-124

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:0004853 uroporphyrinogen decarboxylase activity MF
GO:0006779 porphyrin-containing compound biosynthetic process BP

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