General information for g6946.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Periodic tryptophan protein 2-like protein.
Parent gene
- The parent gene g6946 is located on chr_2: 20095348..20096229 (+ 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 | g6946 | g6946.t1 | TSS | g6946.t1 | 20093115 | 20093115 |
| chr_2 | g6946 | g6946.t1 | isoform | g6946.t1 | 20093200 | 20096229 |
| chr_2 | g6946 | g6946.t1 | exon | g6946.t1.exon1 | 20093200 | 20093217 |
| chr_2 | g6946 | g6946.t1 | cds | g6946.t1.CDS1 | 20093200 | 20093217 |
| chr_2 | g6946 | g6946.t1 | exon | g6946.t1.exon2 | 20093277 | 20093389 |
| chr_2 | g6946 | g6946.t1 | cds | g6946.t1.CDS2 | 20093277 | 20093389 |
| chr_2 | g6946 | g6946.t1 | exon | g6946.t1.exon3 | 20093447 | 20093670 |
| chr_2 | g6946 | g6946.t1 | cds | g6946.t1.CDS3 | 20093447 | 20093670 |
| chr_2 | g6946 | g6946.t1 | exon | g6946.t1.exon4 | 20093734 | 20096014 |
| chr_2 | g6946 | g6946.t1 | cds | g6946.t1.CDS4 | 20093734 | 20096014 |
| chr_2 | g6946 | g6946.t1 | exon | g6946.t1.exon5 | 20096076 | 20096229 |
| chr_2 | g6946 | g6946.t1 | cds | g6946.t1.CDS5 | 20096076 | 20096229 |
| chr_2 | g6946 | g6946.t1 | TTS | g6946.t1 | 20096303 | 20096303 |
Sequences
>g6946.t1 Gene=g6946 Length=2790
ATGAAGTTTGCGTATAAGTTTAACAACTTATTAGGAACTGTTTACCGAAAAGGAAATTTA
ATTTTCAGTGCAGATGGAAATTCGGTCATTAGTCCAGTTGGAAATCGATTAACAATCTTT
GATTTAAAAAATAATAAATCAAATACATTAGCTATACAAAGTAGTTACAACATTACGGCT
CTTGATTTGTCACCAAATGGTTGTCTGATTGTAGCTTCAAATGAAAATGGAGAGACTTAT
ATGATTAGTACTCTTAGTCAAACAGTTATTCATACATATAAATTTCATAGAGAACCAAAA
TGTATAAGATTTAGTCCAAATGGAAAACTCTTTGCAATATGTATTGAAGAATGTGTGTAT
ATTTTCAAAACACCTGGCATTATCACAGGTCAGTTCAATTCTTTTGTAATTGAACGAATC
TTCAAAGACACTCACGGCGAAAAGATTCATGTTGACTGGTCATATGATTCTCGATTTTTG
GTAGTAGGATCTCGTGATAACACAACAAGAATTTATTCGGTAAAACTTCTTGAAAACTTC
AAATCAGTAGTTTTAAGCGGACATTCTGATTCGGTTGTAACTTGTGCATTTGAGGATAAT
TCATTGAATATTATTATCGTTAGTCGTAATGGACATTTGACTAAATGGGAATGTAGTATG
AAATCCGAAGAAATGTATGAGTTGGAGTATGTTAGAGATGAAGAGCCAACTAATAAAAGA
CAAAAGGAAACTGATTCAGATGAAGAAGAGGATAATTTAAGTGAAGAAGAAGAAAATGCA
GAAAAAATTCAAGAAGATGATTCTGAAAGAGATAAGCAAGGTAAAGTTATACCAGAGACA
GCAGAAAAACCACGTTTTTACTATAAGAAACTTGTTCGCCATTATCTCATGGACGAATTG
AAAAAAGAAAATCGCAATGTGAAACTGACATCAGCATGTTATCATAAGAAATTGAAGCTG
TTAGTTACTGCTTATTCTATAGGTGCATTTTATTTGCACGAGCTTCCAGATGTCTCAATG
ATTCATTCACTTAATATTTCTGACTATGCTATCGATACTGTGACATTTAATTCAACTGGC
GATTGGATTGCATTAGGCGTCTCTGGAGCAGGACAATTACTTGTATGGGAATGGCAGAGC
GAGCAATATATTATGAAACAACAAGGACATAACAATGTTATGAGTTCGCTTACATATTCA
TCGGATGGAAACTTTTTAATCACAGGTTCATATGATGGTAAAGTTAAAGTTTGGAATGTA
ACAAATGGCTTTTGTATTCTCACATTTTCGGAACATACAAGTGGAGTTACTTCAGTGGCA
TTTAGTCGCAATAAAAAGTTCTTTGTTAGTGCTTCATTGGATGGAACAGTAAGAGCTTTT
GATATGTTACGCTATAGAAATTTTCGCACATTAACAGCACCGAGACTTGTACAATTTAGC
TGTGTAGCTATCGATTATTCCGGTGAATTCGTAGCTGCAGGTGCTCAAGATGTGTTTGAC
ATTCATTTATGGTCAATGAAACATGGGAAATTGATGGAAGTATTATCGGGACATGAAGCA
CCTGTGATGACTATAGATTTTTCACCAAATCCCACTTCAAGTGCCTTAGTTTCAGGTGCA
TGGGATCATGAAATTAAAATTTGGAATTGTTTAGAAACATCAAGCGAGCATGAAACAATA
AATATGATGTCAGACGTTGTATGCGTTGCATTTAAACCAAATGGTGAAGAAGTCGCAGTT
GCAACACTCAATGCAAATATTTCTGTTCTTAATATTAAATCGTCACAGCAATTGTATTCA
ATAGAATGTAAAAAAGATATTAGTTTAGGAATTTCCGAAAATGACATTGTTTCTGCAAAG
AAAAATTTTGAGTCTGCATACTTCTCATCAATTGTATATTCGAGTGATGGCGAGTGTATT
TTAGCTGGTGGCAATAACAAATATGTTTGCATTTACCATGTTAAAGAAGGTTTGTTGCTA
AAGAAATTCGAAATTACGCAAAATCTGAGTTTAGATGGAATGTTGGAATTCATTAATCGA
AGAAATATGACCGAGTTTGGTAACATAGCATTAATTGAGGAGAGAGATAAACTTGAAGGC
GGAAATATCAAAATCAAATTACCTGGTACACAGAAAAATGACATAGCTTCAAGAAATTTT
CGACCAGAAGTGGGTGTATCAAGTTTAAAGTTCTCTCCAAATGGACAGCAGTGGTCTGCT
GCGACTACAGAAGGACTTTTAATTTATTCTCTCGATAAAGGCATTGTTTTTGATCCATTT
CAAATGTCAATTGAAGTTACTCCTAAAGCAGCAAGAGAATTGATACATGAACAAGAGTAC
TCTTCTGCTCTCATCATGGCACTAAAATTAAATGAAGTTAATCTCATACAAGAGATTATT
GAACAAATACCGCACACACAAATCGATTTAGTGTTGGATGCTATACCTGAAACTTTCGTT
CGTCGTATAGCAGATTTTATTGCAAAAATTCTCAACTCACACCACATAGAATTTTATTTA
AAATGGACCTGTAGTTTGTTGACAAAATTTGGCCAGAAAAATGAATTGATTGATTCACAA
ATTCTCATAAATCTTCATCAGAATTTAATTCGCAAATACGAAAGCTTAAACCAAATATGT
GAATTTAATAAATATACTATTCGAGTAATCAAAAAAATGTCAAAAGTAAAAATCGACGAG
GAATGTAATGATGACGAAATGTTGCTTATCAATAATAATAATTCAGAAGAAATGGTAAGT
GATATTAATGAAGATACATCAGAAGAATAA
>g6946.t1 Gene=g6946 Length=929
MKFAYKFNNLLGTVYRKGNLIFSADGNSVISPVGNRLTIFDLKNNKSNTLAIQSSYNITA
LDLSPNGCLIVASNENGETYMISTLSQTVIHTYKFHREPKCIRFSPNGKLFAICIEECVY
IFKTPGIITGQFNSFVIERIFKDTHGEKIHVDWSYDSRFLVVGSRDNTTRIYSVKLLENF
KSVVLSGHSDSVVTCAFEDNSLNIIIVSRNGHLTKWECSMKSEEMYELEYVRDEEPTNKR
QKETDSDEEEDNLSEEEENAEKIQEDDSERDKQGKVIPETAEKPRFYYKKLVRHYLMDEL
KKENRNVKLTSACYHKKLKLLVTAYSIGAFYLHELPDVSMIHSLNISDYAIDTVTFNSTG
DWIALGVSGAGQLLVWEWQSEQYIMKQQGHNNVMSSLTYSSDGNFLITGSYDGKVKVWNV
TNGFCILTFSEHTSGVTSVAFSRNKKFFVSASLDGTVRAFDMLRYRNFRTLTAPRLVQFS
CVAIDYSGEFVAAGAQDVFDIHLWSMKHGKLMEVLSGHEAPVMTIDFSPNPTSSALVSGA
WDHEIKIWNCLETSSEHETINMMSDVVCVAFKPNGEEVAVATLNANISVLNIKSSQQLYS
IECKKDISLGISENDIVSAKKNFESAYFSSIVYSSDGECILAGGNNKYVCIYHVKEGLLL
KKFEITQNLSLDGMLEFINRRNMTEFGNIALIEERDKLEGGNIKIKLPGTQKNDIASRNF
RPEVGVSSLKFSPNGQQWSAATTEGLLIYSLDKGIVFDPFQMSIEVTPKAARELIHEQEY
SSALIMALKLNEVNLIQEIIEQIPHTQIDLVLDAIPETFVRRIADFIAKILNSHHIEFYL
KWTCSLLTKFGQKNELIDSQILINLHQNLIRKYESLNQICEFNKYTIRVIKKMSKVKIDE
ECNDDEMLLINNNNSEEMVSDINEDTSEE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g6946.t1 | CDD | cd00200 | WD40 | 354 | 602 | 4.35963E-45 |
| 12 | g6946.t1 | Coils | Coil | Coil | 239 | 266 | - |
| 10 | g6946.t1 | Gene3D | G3DSA:2.130.10.10 | - | 13 | 247 | 1.9E-20 |
| 11 | g6946.t1 | Gene3D | G3DSA:2.130.10.10 | - | 291 | 476 | 2.8E-35 |
| 27 | g6946.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 276 | - |
| 29 | g6946.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 247 | - |
| 28 | g6946.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 248 | 264 | - |
| 6 | g6946.t1 | PANTHER | PTHR19858 | WD40 REPEAT PROTEIN | 1 | 896 | 0.0 |
| 3 | g6946.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 144 | 172 | 0.034 |
| 4 | g6946.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 387 | 419 | 6.9E-7 |
| 5 | g6946.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 425 | 460 | 4.8E-6 |
| 2 | g6946.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 510 | 549 | 2.6E-5 |
| 1 | g6946.t1 | Pfam | PF04003 | Dip2/Utp12 Family | 791 | 891 | 9.7E-14 |
| 25 | g6946.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 406 | 420 | - |
| 26 | g6946.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 536 | 550 | - |
| 30 | g6946.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 141 | 226 | 11.128 |
| 31 | g6946.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 344 | 600 | 36.754 |
| 32 | g6946.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 387 | 428 | 16.156 |
| 33 | g6946.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 429 | 470 | 12.079 |
| 34 | g6946.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 515 | 549 | 13.616 |
| 18 | g6946.t1 | SMART | SM00320 | WD40_4 | 43 | 83 | 57.0 |
| 22 | g6946.t1 | SMART | SM00320 | WD40_4 | 86 | 123 | 2.2 |
| 20 | g6946.t1 | SMART | SM00320 | WD40_4 | 134 | 173 | 0.31 |
| 14 | g6946.t1 | SMART | SM00320 | WD40_4 | 178 | 217 | 2.1 |
| 23 | g6946.t1 | SMART | SM00320 | WD40_4 | 337 | 377 | 56.0 |
| 17 | g6946.t1 | SMART | SM00320 | WD40_4 | 380 | 419 | 4.9E-8 |
| 19 | g6946.t1 | SMART | SM00320 | WD40_4 | 422 | 461 | 6.3E-9 |
| 24 | g6946.t1 | SMART | SM00320 | WD40_4 | 508 | 549 | 1.2E-6 |
| 16 | g6946.t1 | SMART | SM00320 | WD40_4 | 553 | 591 | 19.0 |
| 21 | g6946.t1 | SMART | SM00320 | WD40_4 | 616 | 653 | 14.0 |
| 15 | g6946.t1 | SMART | SM00320 | WD40_4 | 713 | 750 | 71.0 |
| 7 | g6946.t1 | SUPERFAMILY | SSF63825 | YWTD domain | 20 | 211 | 1.8E-13 |
| 9 | g6946.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 134 | 596 | 1.1E-60 |
| 8 | g6946.t1 | SUPERFAMILY | SSF63829 | Calcium-dependent phosphotriesterase | 561 | 756 | 4.45E-9 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14558 (periodic tryptophan 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.
