General information for g7919.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Spermine synthase.
Parent gene
- The parent gene g7919 is located on chr_2: 27065139..27067191 (- 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 | g7919 | g7919.t1 | TTS | g7919.t1 | 27063778 | 27063778 |
| chr_2 | g7919 | g7919.t1 | isoform | g7919.t1 | 27064007 | 27066755 |
| chr_2 | g7919 | g7919.t1 | exon | g7919.t1.exon1 | 27064007 | 27064175 |
| chr_2 | g7919 | g7919.t1 | cds | g7919.t1.CDS1 | 27064007 | 27064175 |
| chr_2 | g7919 | g7919.t1 | exon | g7919.t1.exon2 | 27064240 | 27064783 |
| chr_2 | g7919 | g7919.t1 | cds | g7919.t1.CDS2 | 27064240 | 27064783 |
| chr_2 | g7919 | g7919.t1 | exon | g7919.t1.exon3 | 27065029 | 27065137 |
| chr_2 | g7919 | g7919.t1 | cds | g7919.t1.CDS3 | 27065029 | 27065137 |
| chr_2 | g7919 | g7919.t1 | exon | g7919.t1.exon4 | 27066474 | 27066755 |
| chr_2 | g7919 | g7919.t1 | cds | g7919.t1.CDS4 | 27066474 | 27066755 |
| chr_2 | g7919 | g7919.t1 | TSS | g7919.t1 | 27066841 | 27066841 |
Sequences
>g7919.t1 Gene=g7919 Length=1104
ATGGCTGCTAACTCAGTTCTACTAGATTTTTCTATAGAACCATCGCGGATTGGTGATGAA
TTATCGCGAAAGGACATCGTGAAAGTGTTCAAAGAAAATTTGGAAAAATATTTTGGCAAT
TTGAAAATTGTTTATGATATGCTTATTGATGATGGTTATATGTGCATTCTAAGTGATAAT
GCTGGCACTATCTTTACTATAAGATTCTTTGGCGAAGGTCTAATTACCGTTAACATCGAG
TATTTTAAGAAGGAAAATGACTCCCAAAGAATTTCATTTGAGTCAACGCGACAACTCGAG
AATGTGCTGGTTAAAGAATTGAATTTATTGCACGGCCAATCATTACCAGCATTGAGTCGT
GGGCCGATTGTAAAATATTTCCCTACTGCAGATGAGCGGATCATTGAGTATGATATTGAC
AAGGTATTATTTGATAAACGTTCTGAATTCCAAAAGATTCAGATCGTGCATTCGAAAACT
CTTGGCAATATGTTGATCCTTGATGAATTGCAAAACATTGCTGAAGCTGATTTGATTTAC
ACTCAAACATTGATGCAACATGGCAAAGAAAATTATGAAGGAAAAGAAATCTGCATTCTG
GGTGGTGGTGATGGTGCTTTGCTCTATGAGTTATTAAAAGAAAATCCTAAACATGTTGTT
ATGCTCGAAATTGATGATCTCGTCATGGAAGCTTGTAACAAGTACATGAATTCAATTTGT
GGCGATGTTCTTGAAACTCGCAAAGGCGATAATTATGAAATTATCGTTGGAGATTGCATG
GTTTGGATTGATAAATATATCAAAGATGGAAAAAAGTTTGACTATGTTTTCGGTGATCTC
ACTGATATTCCAATCTCTGATACGCCAACTGGAGAAATTTGGGATTTTATTCGCACCATT
TTGGAGAAATCTTTTGCTGTCTTGAAACCTGATGGTAAATTCATGACTCATGGCAATGGC
GCATCATGCCCAGAATCTCTTGAGATGTATGAAGAGCAGTTGAAAAAACTTCGACCATGC
GTTAAATTTTCACGCGACACCGCATTTGTTCCATCATTCATGGAGGATTGGATCTTTTAT
CAAGTCACATTTGCTAATCAGTGA
>g7919.t1 Gene=g7919 Length=367
MAANSVLLDFSIEPSRIGDELSRKDIVKVFKENLEKYFGNLKIVYDMLIDDGYMCILSDN
AGTIFTIRFFGEGLITVNIEYFKKENDSQRISFESTRQLENVLVKELNLLHGQSLPALSR
GPIVKYFPTADERIIEYDIDKVLFDKRSEFQKIQIVHSKTLGNMLILDELQNIAEADLIY
TQTLMQHGKENYEGKEICILGGGDGALLYELLKENPKHVVMLEIDDLVMEACNKYMNSIC
GDVLETRKGDNYEIIVGDCMVWIDKYIKDGKKFDYVFGDLTDIPISDTPTGEIWDFIRTI
LEKSFAVLKPDGKFMTHGNGASCPESLEMYEEQLKKLRPCVKFSRDTAFVPSFMEDWIFY
QVTFANQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7919.t1 | CDD | cd02440 | AdoMet_MTases | 200 | 317 | 0.000 |
| 6 | g7919.t1 | Gene3D | G3DSA:2.30.140.10 | - | 121 | 175 | 0.000 |
| 7 | g7919.t1 | Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 | 176 | 365 | 0.000 |
| 3 | g7919.t1 | PANTHER | PTHR46315:SF1 | SPERMINE SYNTHASE | 1 | 366 | 0.000 |
| 4 | g7919.t1 | PANTHER | PTHR46315 | SPERMINE SYNTHASE | 1 | 366 | 0.000 |
| 1 | g7919.t1 | Pfam | PF17284 | Spermidine synthase tetramerisation domain | 132 | 169 | 0.000 |
| 2 | g7919.t1 | Pfam | PF01564 | Spermine/spermidine synthase domain | 179 | 362 | 0.000 |
| 8 | g7919.t1 | ProSiteProfiles | PS51006 | Polyamine biosynthesis (PABS) domain profile. | 120 | 365 | 36.139 |
| 5 | g7919.t1 | SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases | 125 | 362 | 0.000 |
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:0016768 | spermine synthase activity | MF |
| GO:0006597 | spermine biosynthetic process | BP |
KEGG
Orthology
- This transcript has been annotated with K00802 (spermine synthase)
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.
