General information for g6140.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as S-adenosylmethionine decarboxylase proenzyme.
Parent gene
- The parent gene g6140 is located on chr_2: 14465019..14466163 (- 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_2 | g6140 | g6140.t1 | isoform | g6140.t1 | 14450212 | 14466163 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon1 | 14450212 | 14450505 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS1 | 14450212 | 14450505 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon2 | 14451408 | 14451428 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS2 | 14451408 | 14451428 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon3 | 14451596 | 14451688 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS3 | 14451596 | 14451688 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon4 | 14451748 | 14452219 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS4 | 14451748 | 14452219 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon5 | 14464074 | 14464160 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS5 | 14464074 | 14464160 |
| chr_2 | g6140 | g6140.t1 | exon | g6140.t1.exon6 | 14466048 | 14466163 |
| chr_2 | g6140 | g6140.t1 | cds | g6140.t1.CDS6 | 14466048 | 14466163 |
| chr_2 | g6140 | g6140.t1 | TSS | g6140.t1 | 14466445 | 14466445 |
| chr_2 | g6140 | g6140.t1 | TTS | g6140.t1 | NA | NA |
Sequences
>g6140.t1 Gene=g6140 Length=1083
ATGGCGAATAATAATTTACTAGATAATATAAACCCCAATTTTTTCGAAGGGGTTGAGAAG
CTCCTGGAAATATGGTTTGCTCCGAATGCCAATGCAGATTTGAGGAAAATTCCAAGATCT
CATTGGGACGCATTACTTAAATCCGTTCGTTGCGAAATCATCAGCTTCACACGCAATGAG
CAAATTGACGCTTACGTCCTGAGTGAGAGCAGCATGTTTGTTTCCAAGCGAAGATGGATT
TTAAAGACATGTGGCACAACCACACCACTACAGTGCTTGGAACCGCTTTTGCAGATGGCA
TTTGAAATTGGCGGTTATTCTGAGATCGAAGATTTGTTTTACTCGCGCAAAAATTATAAA
AAGCCAGAATTGCAGGTGTCACCACATCGTGGATTTGAAGAAGAAGTCGCTTTCCTCGAT
CAATTTTTTGATGACGGTCGCGCCTACTGCTTAGGCTCGGTCAACCGCGATTGTTGGTAT
TTGTACACTCTCAGCAGACGTGGTGTGGGTGAGGCTTTAGTCAATGAAATGTCGCTTGCC
AACAACATGATTATTGAATCACTTGAGGTTCCGGATCCTGATCAAACAATTGAAGTGTTG
ATGACTGATTTAGACCCAAAGGTCATGGCAATTTTCACCAAACCCAATTCATCTGATGCA
AAAGAAGCAACTCTTCAATCTGGAATCAACAAGATCATTCCAGGAATGATAATCGATGAC
TATCTCTTCGATCCATGCGGCTATTCAATGAATGGAGTTTCAAAGAACATTGGAAAAATG
TATAGTGAAGGTTGCTACATGACAATTCACATAACACCTGAACCTGACTTCTCGTATGTC
AGCTTCGAGAGCAACATTGCTGCATCTAGTTACAGTGATTTGATTTCGCGAGTAATTGAT
ACTTTCAAGCCGGGAAAGTTTATCGTCACTGTGTTTGCCAATAAAACTTCGCCAGCATTT
GGTGCGTCTCGCGAACTCGAGCATATTGCGAACATTGGTCAATTTAAGCGTCGTGACATT
CAATACTGTCGCTTTGATTCTTATGATTTGACCTATGCGCACTACATTAAATACCCAAGC
TGA
>g6140.t1 Gene=g6140 Length=360
MANNNLLDNINPNFFEGVEKLLEIWFAPNANADLRKIPRSHWDALLKSVRCEIISFTRNE
QIDAYVLSESSMFVSKRRWILKTCGTTTPLQCLEPLLQMAFEIGGYSEIEDLFYSRKNYK
KPELQVSPHRGFEEEVAFLDQFFDDGRAYCLGSVNRDCWYLYTLSRRGVGEALVNEMSLA
NNMIIESLEVPDPDQTIEVLMTDLDPKVMAIFTKPNSSDAKEATLQSGINKIIPGMIIDD
YLFDPCGYSMNGVSKNIGKMYSEGCYMTIHITPEPDFSYVSFESNIAASSYSDLISRVID
TFKPGKFIVTVFANKTSPAFGASRELEHIANIGQFKRRDIQYCRFDSYDLTYAHYIKYPS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6140.t1 | Gene3D | G3DSA:3.60.90.10 | - | 11 | 359 | 1.3E-128 |
| 2 | g6140.t1 | PANTHER | PTHR11570:SF0 | S-ADENOSYLMETHIONINE DECARBOXYLASE PROENZYME | 10 | 357 | 9.8E-125 |
| 3 | g6140.t1 | PANTHER | PTHR11570 | S-ADENOSYLMETHIONINE DECARBOXYLASE | 10 | 357 | 9.8E-125 |
| 8 | g6140.t1 | PIRSF | PIRSF001355 | SAM_decarbox_euk | 2 | 360 | 3.7E-121 |
| 1 | g6140.t1 | Pfam | PF01536 | Adenosylmethionine decarboxylase | 13 | 355 | 2.7E-118 |
| 5 | g6140.t1 | ProSitePatterns | PS01336 | S-adenosylmethionine decarboxylase signature. | 64 | 74 | - |
| 4 | g6140.t1 | SUPERFAMILY | SSF56276 | S-adenosylmethionine decarboxylase | 14 | 356 | 4.05E-113 |
| 7 | g6140.t1 | TIGRFAM | TIGR00535 | SAM_DCase: S-adenosylmethionine decarboxylase proenzyme | 15 | 357 | 4.8E-94 |
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:0004014 | adenosylmethionine decarboxylase activity | MF |
| GO:0006597 | spermine biosynthetic process | BP |
| GO:0008295 | spermidine biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01611 (S-adenosylmethionine 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.
