General information for g10938.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Partitioning defective 3-like protein.
Parent gene
- The parent gene g10938 is located on chr_1: 12871986..12877989 (- 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_1 | g10938 | g10938.t7 | TTS | g10938.t7 | 12871481 | 12871481 |
| chr_1 | g10938 | g10938.t7 | isoform | g10938.t7 | 12871986 | 12875264 |
| chr_1 | g10938 | g10938.t7 | exon | g10938.t7.exon1 | 12871986 | 12872033 |
| chr_1 | g10938 | g10938.t7 | cds | g10938.t7.CDS1 | 12871986 | 12872033 |
| chr_1 | g10938 | g10938.t7 | exon | g10938.t7.exon2 | 12872093 | 12872465 |
| chr_1 | g10938 | g10938.t7 | cds | g10938.t7.CDS2 | 12872093 | 12872465 |
| chr_1 | g10938 | g10938.t7 | exon | g10938.t7.exon3 | 12873459 | 12874029 |
| chr_1 | g10938 | g10938.t7 | cds | g10938.t7.CDS3 | 12873459 | 12874029 |
| chr_1 | g10938 | g10938.t7 | exon | g10938.t7.exon4 | 12874095 | 12875264 |
| chr_1 | g10938 | g10938.t7 | cds | g10938.t7.CDS4 | 12874095 | 12875232 |
| chr_1 | g10938 | g10938.t7 | TSS | g10938.t7 | NA | NA |
Sequences
>g10938.t7 Gene=g10938 Length=2162
GTAAAACTGGTTCTGCAAATCCAAATACATCAATGAATACTAAGCATGACGGAGACTTAG
GAATTTTTATTAAAAGTGTGTTACATGGAGGAGCTGCAAGCAGAGATGGTCGTTTGAAAA
TGAATGATCAATTACTAAGTGTTAATGGAATTTCATTACTGGGTCAATCAAATGCTGATG
CCATGGATACATTGAGAAGAGCGATGTTACAGACAGGTGGCAAACATCCAGGAGTTATTG
TTTTAAAAATAGCAAGACGTGCTTCATCACGACCAAATAGCACAATTGAGAATGGTGAAC
AACATGTTGTTGACAGTAGTGGAAATACAAGTGAACAGTCAGGATCGACGGTCATTTATT
TATCGCCAAATGACAAGAATTCAGTGAATCAACAGAAAGAGCAACAAATGAGTCCAAATA
CTCCACAAGAAAATGGCAAAAGATGGAGTAATCCAGTGTTGGATCGTTTAACTGGTGGAA
CAGGCAATTCAAGAGTTCAATCAACGCTCATTCAAATGCCAGGTGGTTTAAGAAATGATA
GCTATTATATGGCAACAAATGAAAATTGGAGTCCAAATGTAAATCTTAATAACAGTAATG
GTGTGTTGATTGAAGAAGATTCTGAACCAACTTCACCAATTCTTCCAATAAGACCTGATT
TTCAACATCAAATTTCTGCTTCAACACCAACAAGTGCTGGTGATATTACATATGCGAGTC
AATTATCACTTGAAAATCCAGTTGATGCTTTTAGTCGTGATGCTATTGGAAGAAGAAGTA
TGTCAGAAAAACATCATGCAGCACTTGATGCAAAAGAAACTGGCACATATCAACGAAATA
AAAAGATTCGTGAAGAAAGAGAAAAAAGTAGACATGTATCAAAAACAAATTCTCAGATTC
ACAGTTCAATTGAATCTCTGACAAATATGAATCGAATTGGAAGTATGAAGACAAGACAAA
AATCAGATTTAAGATCAGAAGCAATGGATAAAGTGACTGATCTCGGTCCATCATTGGGCA
TGAAAAAATCATCAAGTCTCGAATCACTTCAAACAATGGTGCAAGAAATTCAAATGTCAG
ATGAACCACGTGGACCAAATGCTTTAAGAGCACCAAGAGGACGTGGTAGAGAAGAAATTC
TTCGTGCAGCTGTAGAAAGACCTGAATCACAACCACGAAAACATTGGTTATTAGAAGAAA
ATGGCACAAATGATAATGATGGTGGATTTTCAAATCGAGGAGGAACATTGCAATCATCAA
CAAATGAAGGAAAAATTAAAGATCAAAAGAAAGGTTTTCTTAAGGGTATTGGGCATATGT
TTAGATTTGGAAAGCATAGAAAAGACGTATATCCGGCACAAACAGAAGTCATTACTGATT
ATACCAGTTGGTCAAATGATGTTTCAGCAAAGAGTGCAACTCTTGGTTCATCAGTTGTCT
CATCGCCATCTGTAAACTCGAATACTTCACAACAAGTTCATAGTCATAATTCATCACATC
AAACAAATTCACAAAATCAAAGTCTTCATCATCATCAACAGCAACAGCAGCAAAAACAAC
AACATAGAGAGCCAAGTCATGAAAGACAACTTTCGGGAAATTCTTCCAATGGTCCGCCAT
CATATCATGCACCTCCAACAATGCTCAATGGACACGGAAACAGTAAAATTACTCAAAATG
ATTTATTTAATCATAGATATTCCCACTATGTCAATTATGATGAGCTTCAACTACAAATTA
GTCGTCGAAATCAGCACTATCACTCACAGCGCTCAGCGCGTAATGTTGATTTGACACATT
TTCATCAATATAACGGTTTGGCACCAATTGCAAATGGTCATAAATATCCGCACCCAGCTC
AGCAACAACAACAACCACAATCAATGCAGCAGCACCATATGCGTCCAATTTCAAGCTATT
ATGAATATGAAACGATAAATCCAAATGGACATTACAGAAAGCTTGGTGAGCATTTTATTC
CACTACAGAACAGTAATAGCAGCAGTAAAATCATCAATGGAACGAGCTCAGTGAGAGTTT
CTGGTTCAACACAACAGAGAGGTCCGATTCCCGACATGAATATGAAACAACATCGAGGGC
CATTTATCACACAAGTACATATTCGTGATCAAAACGGTAATAAACATCCGTCAGCATCAA
AG
>g10938.t7 Gene=g10938 Length=710
MNTKHDGDLGIFIKSVLHGGAASRDGRLKMNDQLLSVNGISLLGQSNADAMDTLRRAMLQ
TGGKHPGVIVLKIARRASSRPNSTIENGEQHVVDSSGNTSEQSGSTVIYLSPNDKNSVNQ
QKEQQMSPNTPQENGKRWSNPVLDRLTGGTGNSRVQSTLIQMPGGLRNDSYYMATNENWS
PNVNLNNSNGVLIEEDSEPTSPILPIRPDFQHQISASTPTSAGDITYASQLSLENPVDAF
SRDAIGRRSMSEKHHAALDAKETGTYQRNKKIREEREKSRHVSKTNSQIHSSIESLTNMN
RIGSMKTRQKSDLRSEAMDKVTDLGPSLGMKKSSSLESLQTMVQEIQMSDEPRGPNALRA
PRGRGREEILRAAVERPESQPRKHWLLEENGTNDNDGGFSNRGGTLQSSTNEGKIKDQKK
GFLKGIGHMFRFGKHRKDVYPAQTEVITDYTSWSNDVSAKSATLGSSVVSSPSVNSNTSQ
QVHSHNSSHQTNSQNQSLHHHQQQQQQKQQHREPSHERQLSGNSSNGPPSYHAPPTMLNG
HGNSKITQNDLFNHRYSHYVNYDELQLQISRRNQHYHSQRSARNVDLTHFHQYNGLAPIA
NGHKYPHPAQQQQQPQSMQQHHMRPISSYYEYETINPNGHYRKLGEHFIPLQNSNSSSKI
INGTSSVRVSGSTQQRGPIPDMNMKQHRGPFITQVHIRDQNGNKHPSASK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g10938.t7 | CDD | cd00992 | PDZ_signaling | 6 | 74 | 2.2399E-13 |
| 5 | g10938.t7 | Gene3D | G3DSA:2.30.42.10 | - | 1 | 78 | 4.3E-21 |
| 9 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 104 | - |
| 12 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 137 | - |
| 15 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 138 | - |
| 10 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 284 | - |
| 16 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 317 | - |
| 14 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 285 | 306 | - |
| 17 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 392 | 418 | - |
| 13 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 393 | 412 | - |
| 8 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 528 | - |
| 11 | g10938.t7 | MobiDBLite | mobidb-lite | consensus disorder prediction | 468 | 504 | - |
| 2 | g10938.t7 | PANTHER | PTHR16484:SF17 | BAZOOKA, ISOFORM B | 4 | 702 | 6.8E-102 |
| 3 | g10938.t7 | PANTHER | PTHR16484 | PARTITIONING DEFECTIVE 3 RELATED | 4 | 702 | 6.8E-102 |
| 1 | g10938.t7 | Pfam | PF00595 | PDZ domain | 4 | 56 | 2.3E-9 |
| 18 | g10938.t7 | ProSiteProfiles | PS50106 | PDZ domain profile. | 1 | 57 | 14.416 |
| 7 | g10938.t7 | SMART | SM00228 | pdz_new | 3 | 77 | 6.4E-5 |
| 4 | g10938.t7 | SUPERFAMILY | SSF50156 | PDZ domain-like | 4 | 76 | 6.66E-18 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
