General information for g1820.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Period circadian protein .
Parent gene
- The parent gene g1820 is located on chr_3: 13181623..13187154 (+ 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_3 | g1820 | g1820.t2 | isoform | g1820.t2 | 13180245 | 13184243 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon1 | 13180245 | 13180426 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS1 | 13180245 | 13180426 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon2 | 13180502 | 13180662 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS2 | 13180502 | 13180662 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon3 | 13180722 | 13180977 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS3 | 13180722 | 13180977 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon4 | 13181054 | 13181104 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS4 | 13181054 | 13181104 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon5 | 13181222 | 13181263 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS5 | 13181222 | 13181263 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon6 | 13181324 | 13181625 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS6 | 13181324 | 13181625 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon7 | 13181677 | 13181889 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS7 | 13181677 | 13181889 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon8 | 13181993 | 13183467 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS8 | 13181993 | 13183467 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon9 | 13183523 | 13183606 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS9 | 13183523 | 13183606 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon10 | 13183677 | 13183985 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS10 | 13183677 | 13183985 |
| chr_3 | g1820 | g1820.t2 | exon | g1820.t2.exon11 | 13184040 | 13184243 |
| chr_3 | g1820 | g1820.t2 | cds | g1820.t2.CDS11 | 13184040 | 13184243 |
| chr_3 | g1820 | g1820.t2 | TTS | g1820.t2 | 13184388 | 13184388 |
| chr_3 | g1820 | g1820.t2 | TSS | g1820.t2 | NA | NA |
Sequences
>g1820.t2 Gene=g1820 Length=3279
ATGGAAGGAACAGAGTCAACACATAACACAAAAATCTCAGATTCAGCTTACAGTAACTCG
TGTAGCAACAGTCAATCGCAAAGAAGTGGAAGTTCAAGTAAATCGAGACAGAGCAATTCA
TCGGGTTCGTCATTCAATTCATCAGGCTATGGTGGGAAGCAACAAAAACCAAATATCGAA
AGAGGAGCAATTCCCCAACCACTTTCAAAGCGTTCATCCAAGGATCGAAAAAAGAAAAAG
TTGAAAAGTGTGATTCAAGTCGGTTCAAGCATTAATGATGATACACAAGCTAATGCTTCA
ACGGAAAGTAAAGGTGATGATGAGATAACAGAAAATGCTACAGAAGAGAAAAATGAAAAA
CAAGAGCTTGTGACAGAATCATCTTCACATACGAGTGTTGAAAACAATATTCCACCTGCT
TCATCGCCGATTCTCAAAAAATCAATAGACGAAGATTTAAAAACGCAAAATGTTGATGGA
ATAACGGACATTGGTGCAATTAACCAAACTGATCAAAATCAAGCAACAAAAGTCGAAAAG
GGAGGTCCCGTTGAGGAAGGATTTTGTTGCGTAATGAGCATGCATGATGGTGTTGTTTTA
TATACAACGCCGTCATTATCTGCTGTTTTGGGCTTTCCTAGAGACATGTGGCTAGGACGA
AGTTTTATTGATTTTGTGCATCCGAAGGATAGACCAACTTTTGCATCACAAATTACAAGT
GGTGTTGCACTTACTGAGGCGAATAGTAACTTCAAAGATACAAAACATTCGCTGTTTGTA
ATGATTCGAAGATATAGAGGTCTTAAGTCGTGTGGCTATGGAATAACATCAAAATCTGTA
AGTTATGAACCTTTTAAGCTAACACTCACATTTCGCGAAGCTCCAGATGAAAATTGGATA
TCAACTGAACATGTTCAATGTAGAAGCACACCGACAGTAAACTCTTCTATGCTTCTCGTA
ATTAGTGCAACACCTGTGAAGAGTGTGTATAAAACAAGTGATGAAGTTTTTACTGCTCAA
CGGGAAAACATGAAATTTACAACACGACACACTGCAACTGGCATCTTAAGTCATGTTGAT
GGAACTGCGCATCTTTTGGGATTTCTTCCTCAAGATATGTTATCTCGTAATATTATGGAT
TTCTATCACCCTGATGACATGCTTCTTTTGAAGGAAGTATATGAGACTATTATGGTAAAA
GGGCAAGGTGCTTCATTTTGTGGAAAACCATATCGATTTCTTACACATAACGGCTATTAC
ATAACAGTAGAAACAGAATGGTCAATTTTTGTTAATCCATGGTCACATCATCTTGAATTT
GTAATAGGCCATCATCGTGTACTTCGTGGACCTTCAAATCCCAATGTGTTATTAGCTGCA
AGTACAACTGAAACTCAATCACAATTTCCAGAGTCAACTTTAAACGAATGCAAAATCATT
CGTGAAGAAATATTGAAACTTTTATCAGAGCCAGTTATAAGACCAAATGATACAGTAAAA
CAACAGGTATCGAAGAGATGTCAAGCACTGGCTAGTTTTATGGAAACGTTAATGGATGAA
GTTACAAAATCAGGTTCACGCGCTGACTTAAAGCTTGATTTGCCTCAGGAGTCTGACCTC
ACATTTTCGGAACGTGATAGTGTTATGCTTATCGGGGAAATTTCTCCACATCATGATTAT
TTCGATTCCAAATCTTCGAGTGAAACACCTCCAAGTTATAATCAATTGAATTATAATGAG
AACCTTCAGCGTTTCTTTGATAGTCGACCTGTGACTGTCATTGAACCTGATATGAAAATG
GACCAAACTGATACAGAAGCTGAGACTAGAACAAATCTAAGTCCCACACAATGTTTTGGC
GAGAGTGGAGGATCGGAGAGTGCCGGTAATATGAGTTCAGCAAGTAATGCAAACATGGAA
AGTATTACGAATACATCAACGGGTACATCAAATGGCAGTTATATACCACCTGCTTTGACT
GAGGCACTTTTATGTAAACATAATGAAGATATGGAAAAAATGATTATAAAACGACATAAA
GTTTCGAGAACTAACAAAGGTGAAAAGAGTAAAAAGAATCAAGATCCACACATTCAACAT
GGTGTTAAAAGATCTGGTTCACATTCATGGGAAGGAGGTGAAATCCATAAGACATCAAAA
CAACAGCATATAGTGGAAAGTCAAAAATCAACAGTAACACCATTTCCCAATCAAACAAAT
CCTCAACCATTTCAAAATGCCAATGTGGATTTATGGCCACCATTTTCTGTGAGTTTAACG
ACAATTCAAAGCACGCACACAACGGCACATGCAACACACTTTGCTACATCATCCATCTTT
CCTACGGTTTATTACATTCCTCAAAATATTTCACCACAAGATCAACAACATGGACAAATA
CCTTTACAATATATGCCTCATAGTGTTCTCTATCATACACTATATCCACATCCATCAACA
TTTTATCATCAAATGCAGTTTCAACCGGCACCAGTTTCACAAGGCATTAGTGAATCAATT
TACAATGCAGCTACATTTCAATTTGATAAAAGTAACTTGGGAATTTTACAAAAAATTCCA
ACTCCTAGTGGATCCCAAAATCAAACATTTCAACGTCCACCATCTCAAGCTACTTCGGTA
AAAGCTGATATGGGCTCTACTTCAGCTTCTGTAGTTAATAGAGCGCTCTCGGAAACTTCT
AAAAAGGGAGGTCAATTGGATTCACCAGCGATTGATACAACAATTGATAACCGCAACAAT
GACAAGACAACAAGTGGAACAACAGGCACAAGCGAAGATGAATCTAGTCATTCGAGTTTT
TACTCATCATTCTTGAAAACAGATGAAGGACCGACATCGTCAAATGAAGGACGTAATGAG
AAAGATAAATATGACTCGATGAAAGATGAAATGCAATGGGAAAAAGGACCCAAAATACCA
GTAAAAAGACCTAATCCGCATTGGCTAGAAAATATTAATTTAACTAACGAGCTCATTTAT
CGTTATCAAGTTAATTCTAAAGTTTTGGCAGATGTTTTAAATGAAGATATGTATACATTG
AAAAATGTGCATCAGCCGGATTTAGTCAACGATCAATTGCATCAACTGTATCTTGATCTT
GAATTAGAAGGATTGTCAGCGAAGCTCTCTCTTGAATCGACATCATCTTCAGCATCAAGT
GGTGAAGAAAATTTAAATTCAATGAAACAGCGACGTAAAAAATTTCAATATAACAAGCTA
GTGTTAGTTTACGAAGAGAATTGTCCTCTTCCTGATTAA
>g1820.t2 Gene=g1820 Length=1092
MEGTESTHNTKISDSAYSNSCSNSQSQRSGSSSKSRQSNSSGSSFNSSGYGGKQQKPNIE
RGAIPQPLSKRSSKDRKKKKLKSVIQVGSSINDDTQANASTESKGDDEITENATEEKNEK
QELVTESSSHTSVENNIPPASSPILKKSIDEDLKTQNVDGITDIGAINQTDQNQATKVEK
GGPVEEGFCCVMSMHDGVVLYTTPSLSAVLGFPRDMWLGRSFIDFVHPKDRPTFASQITS
GVALTEANSNFKDTKHSLFVMIRRYRGLKSCGYGITSKSVSYEPFKLTLTFREAPDENWI
STEHVQCRSTPTVNSSMLLVISATPVKSVYKTSDEVFTAQRENMKFTTRHTATGILSHVD
GTAHLLGFLPQDMLSRNIMDFYHPDDMLLLKEVYETIMVKGQGASFCGKPYRFLTHNGYY
ITVETEWSIFVNPWSHHLEFVIGHHRVLRGPSNPNVLLAASTTETQSQFPESTLNECKII
REEILKLLSEPVIRPNDTVKQQVSKRCQALASFMETLMDEVTKSGSRADLKLDLPQESDL
TFSERDSVMLIGEISPHHDYFDSKSSSETPPSYNQLNYNENLQRFFDSRPVTVIEPDMKM
DQTDTEAETRTNLSPTQCFGESGGSESAGNMSSASNANMESITNTSTGTSNGSYIPPALT
EALLCKHNEDMEKMIIKRHKVSRTNKGEKSKKNQDPHIQHGVKRSGSHSWEGGEIHKTSK
QQHIVESQKSTVTPFPNQTNPQPFQNANVDLWPPFSVSLTTIQSTHTTAHATHFATSSIF
PTVYYIPQNISPQDQQHGQIPLQYMPHSVLYHTLYPHPSTFYHQMQFQPAPVSQGISESI
YNAATFQFDKSNLGILQKIPTPSGSQNQTFQRPPSQATSVKADMGSTSASVVNRALSETS
KKGGQLDSPAIDTTIDNRNNDKTTSGTTGTSEDESSHSSFYSSFLKTDEGPTSSNEGRNE
KDKYDSMKDEMQWEKGPKIPVKRPNPHWLENINLTNELIYRYQVNSKVLADVLNEDMYTL
KNVHQPDLVNDQLHQLYLDLELEGLSAKLSLESTSSSASSGEENLNSMKQRRKKFQYNKL
VLVYEENCPLPD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g1820.t2 | CDD | cd00130 | PAS | 195 | 241 | 1.32787E-5 |
| 24 | g1820.t2 | CDD | cd00130 | PAS | 346 | 447 | 5.71643E-12 |
| 19 | g1820.t2 | Gene3D | G3DSA:3.30.450.20 | - | 184 | 326 | 1.1E-43 |
| 18 | g1820.t2 | Gene3D | G3DSA:3.30.450.20 | - | 327 | 493 | 3.8E-40 |
| 20 | g1820.t2 | Gene3D | G3DSA:1.20.5.770 | Single helix bin | 496 | 533 | 2.0E-19 |
| 9 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 54 | - |
| 13 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 136 | - |
| 14 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 85 | 99 | - |
| 11 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 100 | 124 | - |
| 15 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 599 | 634 | - |
| 10 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 607 | 634 | - |
| 17 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 678 | 711 | - |
| 12 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 687 | 711 | - |
| 8 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 861 | 952 | - |
| 16 | g1820.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 861 | 965 | - |
| 4 | g1820.t2 | PANTHER | PTHR11269 | PERIOD CIRCADIAN PROTEIN | 1 | 1092 | 3.4E-295 |
| 5 | g1820.t2 | PANTHER | PTHR11269:SF16 | PERIOD CIRCADIAN PROTEIN | 1 | 1092 | 3.4E-295 |
| 2 | g1820.t2 | Pfam | PF00989 | PAS fold | 188 | 253 | 8.1E-7 |
| 3 | g1820.t2 | Pfam | PF14598 | PAS domain | 345 | 449 | 3.4E-13 |
| 1 | g1820.t2 | Pfam | PF12114 | Period protein 2/3C-terminal region | 883 | 1073 | 1.6E-24 |
| 21 | g1820.t2 | ProSiteProfiles | PS50112 | PAS repeat profile. | 196 | 245 | 11.423 |
| 22 | g1820.t2 | ProSiteProfiles | PS50112 | PAS repeat profile. | 365 | 401 | 11.616 |
| 7 | g1820.t2 | SUPERFAMILY | SSF55785 | PYP-like sensor domain (PAS domain) | 186 | 239 | 3.49E-10 |
| 6 | g1820.t2 | SUPERFAMILY | SSF55785 | PYP-like sensor domain (PAS domain) | 346 | 448 | 7.82E-19 |
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:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K02633 (period circadian protein 2)
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.
