General information for g17142.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nucleoprotein TPR.
Parent gene
- The parent gene g17142 is located on chr_4: 12624321..12627083 (- 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_4 | g17142 | g17142.t2 | isoform | g17142.t2 | 12624321 | 12627083 |
| chr_4 | g17142 | g17142.t2 | exon | g17142.t2.exon1 | 12624321 | 12627083 |
| chr_4 | g17142 | g17142.t2 | cds | g17142.t2.CDS1 | 12624321 | 12627083 |
| chr_4 | g17142 | g17142.t2 | TSS | g17142.t2 | NA | NA |
| chr_4 | g17142 | g17142.t2 | TTS | g17142.t2 | NA | NA |
Sequences
>g17142.t2 Gene=g17142 Length=2763
ATGGATGAACTTGTCATAACTTCAATCTCAGGAGCTGAACTATCAGAACCTCAACCATCA
CAAGTAACAGAATCACAATCACCTCAAATAACTGAAATTCAACAAGTCAATGAAAATCAA
TCTTCAAAAAATCTCACTGAAGAACGTGATCGACTTTTGAAAATTCTTGAACGTCGTGAT
TTGGAAATTGAAAGACTTGAGACAGAATTACAAACATCAAAACAACAATTGACATCAGCC
ATTGATGCGAAATGTTCAGCTATTGTAAAATCTGAAGAAGCAAATCAAAAAATGCTTGAA
ATTGATTTCAAAGAAAAACGAATGGAACAAGAAAAATCATTGATGGAAAGTCAAATTAAA
ATGCTAACAAATGATTTAAATCGGAATGTTCAAGAACTTCAACAACTTCGTATGGATTCA
TCAACAAGAATTGTCACATTGGAAGGAAAATTACATGAAAAAAGTGAAGAACTCAACATT
TTGACTTTACAATCATCACAATTGCGTGAATCAAATGAAACTTTGACAAATAAAGTCAAA
GAATTGTCACAAAATATTTTAACACTTAATAATGAATTTTCAATAACAATGAAAAAATAT
CAAAATGAATTGTCTGCAAAAACTCGATTGGTTGAGCTTTATAAAAGTAAAAATGAAGAC
ACAATTAATCAACAGAAGGAAATTACTGATGCTATGGCAGAATTAAAATCTGCACTTAAT
GAAGCAACTGAAGAATATGGAAAACTTGAAACAAAAGCTAAAGCTGATGAAGTTCAACAT
CAACTTGACATTTCCGCTCTTAACAGTGTCATTGAAGAACTTAAAACTGAACTTCGTCAT
GCAAATCATTTATTGAATGCTTTGAAGCAGGAAAATGTTCAAATTGCTGTTGAAAAAATT
TGTCCAAGTGTCAGTAAAAATCGTCATTCAATAAGTTCAGTTTATTCAATGTATGTCAAT
GCAAATGAAGATTATGAGCAACTTTCAGTCGAACATGAACAGCTAAAACATCAATTTTCA
CGAGTTGTCGATGAAATTAAAGACAAAGCACCACAAATTCAAAGAACTCAAATTGAATTG
ACAAAATTAAAAGAAGAAAATGAAGAAATGCAAGCCTTTTGTGATTCATTAAAAATTGAT
CGACTTATGTCACAAGAAAAAATCAATGGATTGTTGCAAGAAGTGACAAAATTGAGTCAA
AAAGTTAAAGAATTGCAGCAAGAAAAAACTTTAATGAGTCATCAAGTTTGTGAACTTTTG
AGTTCAATTGAAGGAAAGAAAAATGATGAAAATAAGAAAAGTGATTTTAGTACTTTTAGA
AATATTGAGGAACTTCAGCAAAATAATGTGCAATTGGTGAATTTAGTTAGAGAATTGACA
GCATCAATTGAAGAACTTGAAAAGAAAAAAGATTTGAAAATTGATGAGAGTCAAAATTTA
AAATCATCAAAAATTGAAAGTCAATCAGCTAAAATTGACGGACAAATTTCAAAAACTGAA
AATTCAATGCCAAACCAGCAGAATGAATCAAATTTAGCTCAATCTTACTCAGATAGTCTA
AAAGAAAAGATAAAAATACAACAAACCCAAATTGAATCACTAAACAATCAATTGACTTCC
CTAAAAACTCAACTTACAGAAGTTCAGTCATTAAATTTCAAATTAAAATCACAACTTGAA
CATTCTGACGGTCAATTGAAGCTTCAACAAAAAAATTTCGAAATGATGAAAAAGAAAATG
CAAACTGTAGATGAAAAGAACCAAAATTCAATGACAACAATTGCAAAATTAGAAACAACT
TTGGTGCATTTAAGAGAACAACTTCGTGATACAACAATGAAATTGACAAAAACTGAAAAT
TCACTTGCAAGTATCAATTATGAAAATAAAACTTTAGTTCGAAGTGAAGCACAAAATCGA
GCAAAAATTGAAACACAGGAAAAACAATCAAAAATTAATGGACATTTGATAACAAATTTG
GAATTCATTCGTTCATCAATTGAAAGAATTGAAAATTCAGGAAGTGCATTGAAATTGAAA
GAAAAATGTGAAGAACTTGAGCAGCAACTTGAGGAAGAGAAAAATAAATTAAAAGATTTT
GAAAGTCAAGCAAATGCAGAAATTGAACAACTTGAATGTGAAACGCAATTAATGCAAGAT
GAAATTTCAAAATTGAAAGAAATTTGTGAGAAAAAATCGACAGAAATTGAAAAATTGAGT
GAAAAAATTGCAAAATTTAAGAAGATTGGTGAAAGTGAGCAATCAGACAGTTCAGAAAGT
GACACTGAAGTTGCAAGATTGAAAGAAAATGTTCAAAAATTGAGAAAAGTTGGTAAGCAA
TATCGTCAAGAATGTTTTGAACTCCGCAGTCAACTTGAGGAAGCAAAAGTTAAAAATGAA
GAACTTCAAAATTCAAAAGCTAAAGAAGAATCAATGAGAAATTTATTGACAAAAGCAAAA
AGCATGATTACAAAATTAAATGAAGAAAAAGATCAATTGAAACAAAAATTAAAAGCTGAA
ACTAGCGAATTTTTATCATGTGAAAGTCAAGACATAACTTTGACTGATTTGAATGTTAGT
TTTGCTAGAGATGAAATTCCAAGGACAAGCACAAAGAAAAGAGCTCGCAGTGATGATGGT
GATGATGATGATGTGATTATTTTAGAATGTAGTGAGAAGAAAATTAAGAGTGAAGAGATT
AAAGAAGTTGGAAATATTGAGATAAAGGAATTTTATGGTTGTAAATATCCAATGATGGAA
TAG
>g17142.t2 Gene=g17142 Length=920
MDELVITSISGAELSEPQPSQVTESQSPQITEIQQVNENQSSKNLTEERDRLLKILERRD
LEIERLETELQTSKQQLTSAIDAKCSAIVKSEEANQKMLEIDFKEKRMEQEKSLMESQIK
MLTNDLNRNVQELQQLRMDSSTRIVTLEGKLHEKSEELNILTLQSSQLRESNETLTNKVK
ELSQNILTLNNEFSITMKKYQNELSAKTRLVELYKSKNEDTINQQKEITDAMAELKSALN
EATEEYGKLETKAKADEVQHQLDISALNSVIEELKTELRHANHLLNALKQENVQIAVEKI
CPSVSKNRHSISSVYSMYVNANEDYEQLSVEHEQLKHQFSRVVDEIKDKAPQIQRTQIEL
TKLKEENEEMQAFCDSLKIDRLMSQEKINGLLQEVTKLSQKVKELQQEKTLMSHQVCELL
SSIEGKKNDENKKSDFSTFRNIEELQQNNVQLVNLVRELTASIEELEKKKDLKIDESQNL
KSSKIESQSAKIDGQISKTENSMPNQQNESNLAQSYSDSLKEKIKIQQTQIESLNNQLTS
LKTQLTEVQSLNFKLKSQLEHSDGQLKLQQKNFEMMKKKMQTVDEKNQNSMTTIAKLETT
LVHLREQLRDTTMKLTKTENSLASINYENKTLVRSEAQNRAKIETQEKQSKINGHLITNL
EFIRSSIERIENSGSALKLKEKCEELEQQLEEEKNKLKDFESQANAEIEQLECETQLMQD
EISKLKEICEKKSTEIEKLSEKIAKFKKIGESEQSDSSESDTEVARLKENVQKLRKVGKQ
YRQECFELRSQLEEAKVKNEELQNSKAKEESMRNLLTKAKSMITKLNEEKDQLKQKLKAE
TSEFLSCESQDITLTDLNVSFARDEIPRTSTKKRARSDDGDDDDVIILECSEKKIKSEEI
KEVGNIEIKEFYGCKYPMME
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g17142.t2 | Coils | Coil | Coil | 49 | 83 | - |
| 19 | g17142.t2 | Coils | Coil | Coil | 105 | 139 | - |
| 6 | g17142.t2 | Coils | Coil | Coil | 165 | 192 | - |
| 17 | g17142.t2 | Coils | Coil | Coil | 197 | 217 | - |
| 14 | g17142.t2 | Coils | Coil | Coil | 225 | 259 | - |
| 5 | g17142.t2 | Coils | Coil | Coil | 264 | 291 | - |
| 15 | g17142.t2 | Coils | Coil | Coil | 318 | 338 | - |
| 7 | g17142.t2 | Coils | Coil | Coil | 353 | 380 | - |
| 13 | g17142.t2 | Coils | Coil | Coil | 388 | 415 | - |
| 10 | g17142.t2 | Coils | Coil | Coil | 442 | 483 | - |
| 9 | g17142.t2 | Coils | Coil | Coil | 517 | 551 | - |
| 8 | g17142.t2 | Coils | Coil | Coil | 594 | 614 | - |
| 12 | g17142.t2 | Coils | Coil | Coil | 676 | 749 | - |
| 18 | g17142.t2 | Coils | Coil | Coil | 764 | 843 | - |
| 11 | g17142.t2 | Coils | Coil | Coil | 918 | 920 | - |
| 4 | g17142.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 8 | 29 | - |
| 3 | g17142.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 11 | 29 | - |
| 1 | g17142.t2 | PANTHER | PTHR18898 | NUCLEOPROTEIN TPR-RELATED | 16 | 698 | 5.1E-77 |
| 2 | g17142.t2 | PANTHER | PTHR18898:SF2 | NUCLEOPROTEIN TPR | 16 | 698 | 5.1E-77 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K09291 (nucleoprotein TPR)
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. There were no conditions that were differentially expressed