General information for g5572.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paired box pox-neuro protein.
Parent gene
- The parent gene g5572 is located on chr_2: 10339912..10343132 (- 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 | g5572 | g5572.t1 | isoform | g5572.t1 | 10334033 | 10339912 |
| chr_2 | g5572 | g5572.t1 | exon | g5572.t1.exon1 | 10334033 | 10334200 |
| chr_2 | g5572 | g5572.t1 | cds | g5572.t1.CDS1 | 10334033 | 10334200 |
| chr_2 | g5572 | g5572.t1 | exon | g5572.t1.exon2 | 10334271 | 10334999 |
| chr_2 | g5572 | g5572.t1 | cds | g5572.t1.CDS2 | 10334271 | 10334999 |
| chr_2 | g5572 | g5572.t1 | exon | g5572.t1.exon3 | 10336218 | 10336297 |
| chr_2 | g5572 | g5572.t1 | cds | g5572.t1.CDS3 | 10336218 | 10336297 |
| chr_2 | g5572 | g5572.t1 | exon | g5572.t1.exon4 | 10336371 | 10336511 |
| chr_2 | g5572 | g5572.t1 | cds | g5572.t1.CDS4 | 10336371 | 10336511 |
| chr_2 | g5572 | g5572.t1 | exon | g5572.t1.exon5 | 10339900 | 10339912 |
| chr_2 | g5572 | g5572.t1 | cds | g5572.t1.CDS5 | 10339900 | 10339912 |
| chr_2 | g5572 | g5572.t1 | TSS | g5572.t1 | NA | NA |
| chr_2 | g5572 | g5572.t1 | TTS | g5572.t1 | NA | NA |
Sequences
>g5572.t1 Gene=g5572 Length=1131
ATGCCTCACACAGGTCAGGCAGGAGTGAATCAATTGGGTGGAGTATTTGTGAATGGCAGA
CCACTACCCGATTGCGTCCGACGGCGAATCGTCGAATTGGCATTGATGGGCGTTCGTCCA
TGCGACATTAGTCGACAGCTTTTAGTCTCTCACGGTTGCGTCTCGAAAATTTTAACAAGG
TTCTACGAGACGGGATCTATACGGCCCGGAAGCGTTGGTGGAAGTAAGACAAAGCAAGTT
GCTACACCAACAGTTGTTCGAAAAATTTTACGTTTCAAACAAGAAAATCCTTCAATGTTT
GCATGGGAAATTCGAGATCAATTATTATCTCAACGTATATGCGATCCATCAACAATTCCT
TCAGTCTCATCAGTCAATCGTATATTAAGAAATGGAGGACTTTGGACTGATGATGCTATA
CCTACAAACACTACCAGTATTAATAATAATAATAACAATAGCAGCAGTTCAAATGGTCAG
AGCTCTTCTGCAGAAAGTGATTCATTTTCACAATTAAAAGCTCTCTCAGTTCCTATTCAA
CCAACAATTTATGGAACCAATGATTTTCTTAATTCTTATAAATATTCTTTGGGTGTAAAT
TATTCCTCTACGTCATCAAATGCAACCATCACTTCAAATATTGTTGATTCAGCACAAAAA
TTAGTACAATTTCCAACGTCGCCCATTCCATGTAAAATTCCAGAAAATTATGCCAGTACA
ACAATGTCGGGTAGCAGTAACAATAGTAACTGCAATAATAATATTAATAACAGCACGTCA
TTGTATTACAAACATTGGATATGGAGAAGTCGTAATATTTTCTATCCACAATTAGCTCAT
TTATCATCATATCCTGATATGTCACCACCTAGTAATAAAACTGAATCAACAAATTCTAAT
TCTCCAGCGCAAATAGCTGAAATTAATAGTGATGATTCATTGGATAGCCATGATAATGAA
AAGCTTAAAACAACAACTTCACGAAAAAGAAATCCGTACTCAATTGAAGAATTACTCAAA
AAACCCGAAAAGCGTAGAAAAATTGCTGACGAAAATTTCAATGAAAAAGCAGGAGAAAAT
GAAGTAGAAACTAATGAAGAAGTGAATTTAAATGTTGATGTTTGTGATTAA
>g5572.t1 Gene=g5572 Length=376
MPHTGQAGVNQLGGVFVNGRPLPDCVRRRIVELALMGVRPCDISRQLLVSHGCVSKILTR
FYETGSIRPGSVGGSKTKQVATPTVVRKILRFKQENPSMFAWEIRDQLLSQRICDPSTIP
SVSSVNRILRNGGLWTDDAIPTNTTSINNNNNNSSSSNGQSSSAESDSFSQLKALSVPIQ
PTIYGTNDFLNSYKYSLGVNYSSTSSNATITSNIVDSAQKLVQFPTSPIPCKIPENYAST
TMSGSSNNSNCNNNINNSTSLYYKHWIWRSRNIFYPQLAHLSSYPDMSPPSNKTESTNSN
SPAQIAEINSDDSLDSHDNEKLKTTTSRKRNPYSIEELLKKPEKRRKIADENFNEKAGEN
EVETNEEVNLNVDVCD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5572.t1 | CDD | cd00131 | PAX | 5 | 133 | 1.61848E-81 |
| 12 | g5572.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 1 | 73 | 4.4E-38 |
| 11 | g5572.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 74 | 135 | 1.2E-29 |
| 19 | g5572.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 143 | 165 | - |
| 16 | g5572.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 307 | 376 | - |
| 17 | g5572.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 311 | 327 | - |
| 18 | g5572.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 333 | 363 | - |
| 2 | g5572.t1 | PANTHER | PTHR45636:SF32 | PAIRED BOX POX-NEURO PROTEIN | 1 | 281 | 1.4E-99 |
| 4 | g5572.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 1 | 281 | 1.4E-99 |
| 3 | g5572.t1 | PANTHER | PTHR45636:SF32 | PAIRED BOX POX-NEURO PROTEIN | 325 | 351 | 1.4E-99 |
| 5 | g5572.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 325 | 351 | 1.4E-99 |
| 9 | g5572.t1 | PRINTS | PR00027 | Paired box signature | 9 | 24 | 1.5E-35 |
| 7 | g5572.t1 | PRINTS | PR00027 | Paired box signature | 27 | 45 | 1.5E-35 |
| 6 | g5572.t1 | PRINTS | PR00027 | Paired box signature | 47 | 64 | 1.5E-35 |
| 8 | g5572.t1 | PRINTS | PR00027 | Paired box signature | 65 | 82 | 1.5E-35 |
| 1 | g5572.t1 | Pfam | PF00292 | ‘Paired box’ domain | 5 | 130 | 7.5E-63 |
| 15 | g5572.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 39 | 55 | - |
| 20 | g5572.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 5 | 132 | 61.786 |
| 14 | g5572.t1 | SMART | SM00351 | pax3 | 5 | 130 | 3.7E-86 |
| 10 | g5572.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 7 | 133 | 1.58E-34 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5572/g5572.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5572.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003677 | DNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
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. There were no conditions that were differentially expressed