General information for g10755.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Diaminopimelate decarboxylase.
Parent gene
- The parent gene g10755 is located on chr_1: 11730606..11732023 (- strand)
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 | g10755 | g10755.t1 | TTS | g10755.t1 | 11730438 | 11730438 |
| chr_1 | g10755 | g10755.t1 | isoform | g10755.t1 | 11730606 | 11732023 |
| chr_1 | g10755 | g10755.t1 | exon | g10755.t1.exon1 | 11730606 | 11730733 |
| chr_1 | g10755 | g10755.t1 | cds | g10755.t1.CDS1 | 11730606 | 11730733 |
| chr_1 | g10755 | g10755.t1 | exon | g10755.t1.exon2 | 11730789 | 11730973 |
| chr_1 | g10755 | g10755.t1 | cds | g10755.t1.CDS2 | 11730789 | 11730973 |
| chr_1 | g10755 | g10755.t1 | exon | g10755.t1.exon3 | 11731029 | 11731530 |
| chr_1 | g10755 | g10755.t1 | cds | g10755.t1.CDS3 | 11731029 | 11731530 |
| chr_1 | g10755 | g10755.t1 | exon | g10755.t1.exon4 | 11731591 | 11732023 |
| chr_1 | g10755 | g10755.t1 | cds | g10755.t1.CDS4 | 11731591 | 11732023 |
| chr_1 | g10755 | g10755.t1 | TSS | g10755.t1 | 11732053 | 11732053 |
Sequences
>g10755.t1 Gene=g10755 Length=1248
ATGTCAAAATTTCCTCGATCAACAAAATTTTCAGCTGAAAAACTGATTGAACTGGCAGAA
ATATATAATTCACCTTTTTGGGCATATGATGGTGATATCATCAAAACAAAAGTCGATCAA
CTTAAAAACTTTGATGTCATCCGCTATGCACAAAAGGCTTGTTCAAACATAAATATTTTA
CGATTAATGAAAAGTCTCGGCACGAAAATTGATTCTGTCTCGCCGGGTGAAATTGAAAGA
GCTTTGAACGCTGGTTTTCAAGCGGGAACAGCTGAAAATGAAATTGTATTTACGGCTGAT
GTTATTGACAATGAAACATGCAAAAGAGCGTTAGAATTGAAAATTCCAATCAATTGTGGA
TCAATTGATATGCTGAAAGTATTAGGAACAAAAAAAGCTGAAGGCCATCCTGTATGGATT
AGAATAAATCCAGGTTTCGGACAAGGACACAGTCAAAAGACAAACACAGGCGGTGAGAAC
AGCAAACATGGAATTTGGTATGAAGACTTACCAGAAGCACTAGCTGTAATTAAACAAAAC
AAGCTAAAACTTATAGGATTCCACATGCATATTGGATCAGGTTTATTCTCTAAAAATTTT
GATCGGACTTGTGATGCCATGGCTGAATTAGTCATAAAATGTGATGTTGACATTGAAGCT
ATTTCAGCAGGAGGTGGTATTCCAATTGCTTATAAAGAAAATGAAAATGATGTTGACATT
AATAATTATTACGAGCTCTGGAATGCTGCAAGGAAAAAGATTGAAGAACATTTTGGTCAT
TCAATTACATTAGAAATTGAACCAGGCAGATTTCTAGTTGCTGAATCTGGAATATTAGTT
ACAAAAGTTTTAGCAATAAAACAAATGGGAGGAAAAAAATATGCCCTTATTAATTCTGGA
TTTAATGATCTTATGAGACCAGCTATGTATGGAAGTTACCATCACATAACAGTTCTTGAT
GACACAGAAGACAGAGTAATGGAAGAAATTGTTATTGCAGGGCATTTGTGCGAATCAGGT
GATATGTTTACACAAGGCGAAGGAGGTATTGTACAATTAAGACTTCTTCCAAAACTACAT
GTTGGTGATTATTTGATTTTTCATGATGTTGGTGCATATGGTGCATCAATGTCATCTAAC
TATAATTCATGGCCTCTATTACCAGAAATTCTCTTTATTGATGGTGAGACAAAACTCATC
CGAAGGAAGCAAACAATTCATGATTTAATGCATTTAGAGCAAATTTAA
>g10755.t1 Gene=g10755 Length=415
MSKFPRSTKFSAEKLIELAEIYNSPFWAYDGDIIKTKVDQLKNFDVIRYAQKACSNINIL
RLMKSLGTKIDSVSPGEIERALNAGFQAGTAENEIVFTADVIDNETCKRALELKIPINCG
SIDMLKVLGTKKAEGHPVWIRINPGFGQGHSQKTNTGGENSKHGIWYEDLPEALAVIKQN
KLKLIGFHMHIGSGLFSKNFDRTCDAMAELVIKCDVDIEAISAGGGIPIAYKENENDVDI
NNYYELWNAARKKIEEHFGHSITLEIEPGRFLVAESGILVTKVLAIKQMGGKKYALINSG
FNDLMRPAMYGSYHHITVLDDTEDRVMEEIVIAGHLCESGDMFTQGEGGIVQLRLLPKLH
VGDYLIFHDVGAYGASMSSNYNSWPLLPEILFIDGETKLIRRKQTIHDLMHLEQI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g10755.t1 | CDD | cd06828 | PLPDE_III_DapDC | 22 | 392 | 5.69541E-141 |
| 18 | g10755.t1 | Gene3D | G3DSA:2.40.37.10 | Lyase | 20 | 410 | 1.8E-130 |
| 17 | g10755.t1 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase | 31 | 278 | 1.8E-130 |
| 5 | g10755.t1 | Hamap | MF_02120 | Diaminopimelate decarboxylase [lysA]. | 12 | 414 | 36.390724 |
| 3 | g10755.t1 | PANTHER | PTHR43727:SF2 | DIAMINOPIMELATE DECARBOXYLASE 1, CHLOROPLASTIC-RELATED | 12 | 411 | 4.8E-101 |
| 4 | g10755.t1 | PANTHER | PTHR43727 | DIAMINOPIMELATE DECARBOXYLASE | 12 | 411 | 4.8E-101 |
| 10 | g10755.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 49 | 67 | 1.0E-20 |
| 13 | g10755.t1 | PRINTS | PR01181 | Diaminopimelate decarboxylase signature | 67 | 84 | 3.2E-21 |
| 8 | g10755.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 69 | 81 | 1.0E-20 |
| 12 | g10755.t1 | PRINTS | PR01181 | Diaminopimelate decarboxylase signature | 156 | 165 | 3.2E-21 |
| 6 | g10755.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 181 | 194 | 1.0E-20 |
| 9 | g10755.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 264 | 283 | 1.0E-20 |
| 11 | g10755.t1 | PRINTS | PR01181 | Diaminopimelate decarboxylase signature | 292 | 310 | 3.2E-21 |
| 7 | g10755.t1 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature | 371 | 384 | 1.0E-20 |
| 14 | g10755.t1 | PRINTS | PR01181 | Diaminopimelate decarboxylase signature | 381 | 403 | 3.2E-21 |
| 1 | g10755.t1 | Pfam | PF02784 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain | 42 | 274 | 1.6E-53 |
| 2 | g10755.t1 | Pfam | PF00278 | Pyridoxal-dependent decarboxylase, C-terminal sheet domain | 275 | 371 | 4.9E-25 |
| 20 | g10755.t1 | ProSitePatterns | PS00878 | Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. | 49 | 67 | - |
| 15 | g10755.t1 | SUPERFAMILY | SSF51419 | PLP-binding barrel | 24 | 276 | 3.05E-54 |
| 16 | g10755.t1 | SUPERFAMILY | SSF50621 | Alanine racemase C-terminal domain-like | 249 | 414 | 1.21E-53 |
| 21 | g10755.t1 | TIGRFAM | TIGR01048 | lysA: diaminopimelate decarboxylase | 10 | 413 | 4.0E-120 |
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:0009089 | lysine biosynthetic process via diaminopimelate | BP |
| GO:0008836 | diaminopimelate decarboxylase activity | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01586 (diaminopimelate decarboxylase)
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. There were no conditions that were differentially expressed