General information for g5539.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as histone-arginine N-methyltransferase.
Parent gene
- The parent gene g5539 is located on chr_2: 10169943..10171394 (- 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 | g5539 | g5539.t1 | TTS | g5539.t1 | 10168113 | 10168113 |
| chr_2 | g5539 | g5539.t1 | isoform | g5539.t1 | 10168317 | 10170958 |
| chr_2 | g5539 | g5539.t1 | exon | g5539.t1.exon1 | 10168317 | 10169059 |
| chr_2 | g5539 | g5539.t1 | cds | g5539.t1.CDS1 | 10168317 | 10169059 |
| chr_2 | g5539 | g5539.t1 | exon | g5539.t1.exon2 | 10169475 | 10170104 |
| chr_2 | g5539 | g5539.t1 | cds | g5539.t1.CDS2 | 10169475 | 10170104 |
| chr_2 | g5539 | g5539.t1 | exon | g5539.t1.exon3 | 10170193 | 10170454 |
| chr_2 | g5539 | g5539.t1 | cds | g5539.t1.CDS3 | 10170193 | 10170454 |
| chr_2 | g5539 | g5539.t1 | exon | g5539.t1.exon4 | 10170511 | 10170699 |
| chr_2 | g5539 | g5539.t1 | cds | g5539.t1.CDS4 | 10170511 | 10170699 |
| chr_2 | g5539 | g5539.t1 | exon | g5539.t1.exon5 | 10170806 | 10170958 |
| chr_2 | g5539 | g5539.t1 | cds | g5539.t1.CDS5 | 10170806 | 10170958 |
| chr_2 | g5539 | g5539.t1 | TSS | g5539.t1 | 10171402 | 10171402 |
Sequences
>g5539.t1 Gene=g5539 Length=1977
ATGGTAGTTGGAAAACAACAAGTAAAGAATCGTTCAAGATCAACAATTTTTAGTAAAATG
CAATCATCAGTGATGGGAATGTCTCCCAAGGAGCTATCCGAGAACGATGATTTGGCGACT
TCATTAATATTAGATACAATTCTCGGATTCCAAACACACAAAATGAATACACGATATAAA
CCGCAAAGAATTAATCGAGAGGAACTGAAGAGGATTACAGATGAATTTATTGAAACTCAA
AATTATGACATAGCTATGAGTAAAATAATGTCTGGAGACTGGATTCCAAAAAGTAAGCTT
ACAACAAAGAACAAGCTTGCTCAAAAAAGACTTTATGCTCATATCTATCGATATCTGAGA
GTTTTCGATCAACAATCTGGTTTTGTCATTGAACCTTGCTATCGTTACTCACTTGAAGGA
CAAAAAGGAGCGAAAATTTCATCTACGAAAAAATGGTACAAAAATGAAAAGATTGAATGT
CTAGTGGGCTGTATTGCAGAAATGACTGAAGCTGAAGAGGCATCACTACTGCATCCAGGC
AAAAATGATTTCTCAGTGATGTATAGTTGTCGTAAAAATTGTGCACAACTTTGGCTTGGA
CCTGCCGCATTCATAAACCACGACTGTAGAGCAAATTGCAAATTTGTTCCCACGGGCAGA
GATACTGCATGTGTAAAAGTATTGCGTGATATAGAAATAGGTGAAGAAATCACATGCTTC
TATGGTGAAGACTTTTTTGGTGACAGCAATCGCTATTGTGAATGCGAAACATGTGAACGT
CGATGCAGCGGCGCATTCTCAAAATGGAAGGAGAAGCCGTCAGAAGAAAAGCTACCAGGT
GGCTATCGTCTTCGTGAAACAGACAACCGTATCAATAGGAAAAAGAATTTTTCGCATCAT
GATAGTGACAAATCGGAAACACCAGCCGATACTCAATTGAGTTTTAAAGAACTTAGGAAA
AGATGCACGAAATATGATGCCGAAATGATAATAGCCCAAAGATCGCCAAATTATGTTGAC
GAATCTAATATAACGACGACGACGAGCGCCTCAAAGCAGCCCAGTCACAATCATGCAACT
AGAAATAGCATATTCACTGCCACTAGTAATATAGTAACACGTTCAACTAAACGTCTCAAT
AGCAATGATTCGCCAAAGTCCTTTCTAGGGCGGAAGCAGCCCAATCCGAAGCCATTTCGG
AAGGAAATGATAGACTTTGATAAGAACAGTAATGGCGATGCTGATGTTGATACGGAAAGC
GATACCACCAATTCTTTCAATATTTATAAGAATGATTTTCAAGATGATCAGTTGAATGCT
GGTAGACAACAGAAATCAACTCGATTAAGTGAGAGCGAAAGTTCATCATCGTGGGAAAAT
AAACAATTTCCTAATACAAATAACTTAAATTTGATACCGAATTTTGGTAATAATAGTATT
TTATTAAAGACTCCCGAGAGACGTCTGAAATTGACGATTCGTGTGAAAAGGAGTCCAGCA
TCAAGTAACACCTGCTCGAGTTTCGACCAGAACTTTGGACTGGACGAAAAATCAAACAAC
AAATGTGATGATAATGAGCCAGAATATGAAATTCTAAGAACTGAAGGCATCGATTGCACT
GGAATTAGTGAAAATGAATCTACATCAACACTTATTTTTACTGGTATTAAACGATCAAAA
AGGAAAAAGCGTCACAAGCACAAAAAGAGTAAAAGAAATAAAAAGTTTTCTAATTCAGAT
GAATTTACTAATTATAGTGAGCAAACTTGTAATAATAGCTCAGAGACATCTTCACATTAT
GATGAAACGGAAGAAGACAAGCAACAGAATTATACAAGAGCAAAACGAGTGAAGCTAATG
TTTGGAAATGAAATGAAAATCTTAAACATTCCTGACAAAACATCATCATCAACTTCTGAA
AGTGATCTAAAGTCAAATACTACTAGTTTAATACCAGTTAAATGTTGGGACTATTAA
>g5539.t1 Gene=g5539 Length=658
MVVGKQQVKNRSRSTIFSKMQSSVMGMSPKELSENDDLATSLILDTILGFQTHKMNTRYK
PQRINREELKRITDEFIETQNYDIAMSKIMSGDWIPKSKLTTKNKLAQKRLYAHIYRYLR
VFDQQSGFVIEPCYRYSLEGQKGAKISSTKKWYKNEKIECLVGCIAEMTEAEEASLLHPG
KNDFSVMYSCRKNCAQLWLGPAAFINHDCRANCKFVPTGRDTACVKVLRDIEIGEEITCF
YGEDFFGDSNRYCECETCERRCSGAFSKWKEKPSEEKLPGGYRLRETDNRINRKKNFSHH
DSDKSETPADTQLSFKELRKRCTKYDAEMIIAQRSPNYVDESNITTTTSASKQPSHNHAT
RNSIFTATSNIVTRSTKRLNSNDSPKSFLGRKQPNPKPFRKEMIDFDKNSNGDADVDTES
DTTNSFNIYKNDFQDDQLNAGRQQKSTRLSESESSSSWENKQFPNTNNLNLIPNFGNNSI
LLKTPERRLKLTIRVKRSPASSNTCSSFDQNFGLDEKSNNKCDDNEPEYEILRTEGIDCT
GISENESTSTLIFTGIKRSKRKKRHKHKKSKRNKKFSNSDEFTNYSEQTCNNSSETSSHY
DETEEDKQQNYTRAKRVKLMFGNEMKILNIPDKTSSSTSESDLKSNTTSLIPVKCWDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5539.t1 | CDD | cd19186 | SET_Suv4-20 | 125 | 266 | 4.31105E-100 |
| 6 | g5539.t1 | Gene3D | G3DSA:1.10.10.1700 | - | 18 | 123 | 1.6E-34 |
| 5 | g5539.t1 | Gene3D | G3DSA:2.170.270.10 | SET domain | 124 | 270 | 4.8E-38 |
| 14 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 277 | 310 | - |
| 16 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 277 | 307 | - |
| 12 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 347 | 389 | - |
| 13 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 347 | 398 | - |
| 15 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 428 | 462 | - |
| 11 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 557 | 612 | - |
| 17 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 557 | 573 | - |
| 9 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 579 | 597 | - |
| 10 | g5539.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 598 | 612 | - |
| 2 | g5539.t1 | PANTHER | PTHR12977:SF4 | HISTONE-LYSINE N-METHYLTRANSFERASE SUV4-20 | 21 | 380 | 1.3E-168 |
| 3 | g5539.t1 | PANTHER | PTHR12977 | SUPPRESSOR OF VARIEGATION 4-20-RELATED | 21 | 380 | 1.3E-168 |
| 1 | g5539.t1 | Pfam | PF00856 | SET domain | 175 | 242 | 1.2E-9 |
| 18 | g5539.t1 | ProSiteProfiles | PS51570 | Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. | 3 | 307 | 71.044 |
| 19 | g5539.t1 | ProSiteProfiles | PS50280 | SET domain profile. | 131 | 242 | 11.725 |
| 8 | g5539.t1 | SMART | SM00317 | set_7 | 132 | 248 | 2.0E-18 |
| 4 | g5539.t1 | SUPERFAMILY | SSF82199 | SET domain | 114 | 261 | 5.23E-28 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5539/g5539.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5539.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
| GO:0042799 | histone methyltransferase activity (H4-K20 specific) | MF |
| GO:0034772 | histone H4-K20 dimethylation | BP |
KEGG
Orthology
- This transcript has been annotated with K11429 ([histone H4]-N-methyl-L-lysine20 N-methyltransferase)
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.
