General information for g15624.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paired box protein Pax-2-A.
Parent gene
- The parent gene g15624 is located on chr_4: 6134440..6151594 (- 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 | g15624 | g15624.t1 | isoform | g15624.t1 | 6134440 | 6151594 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon1 | 6134440 | 6134588 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS1 | 6134440 | 6134588 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon2 | 6135093 | 6135209 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS2 | 6135093 | 6135209 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon3 | 6135409 | 6135885 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS3 | 6135409 | 6135885 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon4 | 6136555 | 6136656 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS4 | 6136555 | 6136656 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon5 | 6136772 | 6137105 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS5 | 6136772 | 6137105 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon6 | 6137695 | 6137780 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS6 | 6137695 | 6137780 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon7 | 6138437 | 6138625 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS7 | 6138437 | 6138625 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon8 | 6139249 | 6139325 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS8 | 6139249 | 6139325 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon9 | 6145898 | 6146095 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS9 | 6145898 | 6146095 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon10 | 6146695 | 6146860 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS10 | 6146695 | 6146860 |
| chr_4 | g15624 | g15624.t1 | exon | g15624.t1.exon11 | 6151540 | 6151594 |
| chr_4 | g15624 | g15624.t1 | cds | g15624.t1.CDS11 | 6151540 | 6151594 |
| chr_4 | g15624 | g15624.t1 | TSS | g15624.t1 | NA | NA |
| chr_4 | g15624 | g15624.t1 | TTS | g15624.t1 | NA | NA |
Sequences
>g15624.t1 Gene=g15624 Length=1950
ATGGATTTATCAACGGCATATCGATATAATCAAAATATGATGGAATATTACACATGCCAC
GGCGGTGTAAATCAGTTAGGTGGTGTGTTTGTCAATGGTCGACCACTACCTGATGTCGTT
CGACAGCGAATTGTTGAATTAGCTCATAATGGTGTTCGTCCATGCGACATAAGTCGACAA
CTTCGCGTCAGTCATGGCTGTGTATCAAAAATTTTATCAAGATATTATGAAACGGGGAGC
TTTAAGGCGGGTGTGATTGGTGGAAGCAAACCAAAAGTTGCAACACCACCAGTCGTAGAC
GCAATCGCCAACTATAAACGAGAAAATCCGACAATGTTTGCGTGGGAAATTCGCGATAGA
CTTTTAGCCGAGGGAATTTGCTCACAAGACAATGTGCCGAGTGTGTCGTCCATTAATCGA
ATTGTTCGCAATAAAGCAGCTGAAAAAGCAAAACATCATCATCATCAACAGACACAAAAC
TCAGGAACACCTCCAGGCCACCTCCCACAATCACCACAAATGACAACGACAGATCCGCAA
GACAGTAACGGCGCGACACCAAATTCAGTAAATGGTAGCGAAGGACGAGTATCGAGTGGT
TATAGCATCAATGGAATTCTTGGCATACAACATGCCAATGATGTCAATGTAAATAGCATG
AAAAGGAAAAGAGTTGATGACCATGATGAAAATCGTGACATTAATATTCATATGGAAGAA
GATATTAAGAGACAACGAATTCAATACAACGGAGACCAAATTTATCCAAATCTCTGGTCA
TCAAAGTGGTGTGTAAAAGATGAACCCAAACACCAAGATCTCGTAAACTCAGTAGTCGTA
GCAATGCCAACGCCACCACACAATAATAACAATAGCAGCGCAAATAACAACAACAATAGC
AATTCAAATAACAATACATCGAGCAACAACAATAATAATAATCCATCAGCAAATAACAAC
ACATCATCGTATTATGATACTCATAATGTGTTCCCAACATCGGTCAATAACAACAACAAT
CAAGACACAATACTCTATGATAGCATCACGACGATATCACAAGCACAAAATACCCTTTAT
GCGCCCTCAATTGGAACTGCTATCGGAACAGGAACATTTACGTCATTGGCACCACTCAGT
ATGCAAGATATTAAACTTAATGCAACGACTACTCTAATTGATCAATCGATGTCTCCATAT
CATGCAGATAGTACAACGCCTTACAATACACTCGCAATGTCACAAATTGAAGATGGAATT
CCGCAAGCGACTCAACAAGATCAACCTGATTCATCATCGGAACTGCCAATGTTTACAATG
ATTTCACCTGATGGACAATCGACATCACAAGGTCTTATTAAAAATGACACAAATAATAAC
AACAACGATCGAAATAATAACAAATCAAAGGATAAATTACATCATGATGATGACCATAGC
AAGAGACAATTGTTACAACGTTATAGACTTGAAGATGGTGTTGATCATGCCACAACCATT
CATCATCCTCATCATTTATTACTTTTACAACAGCAACAACAACAAATGAACTCACAAATG
GGTCATTCAATGGATGGAAAATCAAATTTAATTCCAGTACCCGAAAATTCACCATCACTA
ATTGTGCTGCAACCAAGTGCACAAAGTGGTGGTTATTCATCTTTCTTCAATCATTATGCA
ACAGCTAATAATGGATCTGTAGTAGCAGCAAGTGATTATGCTTATAATTCAGCTCCATAC
CAGCAATATAGTACGCCGTATAATTATGGATACAATGTACCCACCACTAGCAGTCTCCTC
AACACAACGTATTATTTCAATAATGAACAAACAAGCGATCTTCGATCTCCACTGGCAGCA
ACACGTGCAAATTCTTTAGCAAGCGCTTCATCGCCAACTGGTGCATGTGTGAAAACTGAA
ATCAGTGCAAAGGACATATTTCTCGTGTAG
>g15624.t1 Gene=g15624 Length=649
MDLSTAYRYNQNMMEYYTCHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQ
LRVSHGCVSKILSRYYETGSFKAGVIGGSKPKVATPPVVDAIANYKRENPTMFAWEIRDR
LLAEGICSQDNVPSVSSINRIVRNKAAEKAKHHHHQQTQNSGTPPGHLPQSPQMTTTDPQ
DSNGATPNSVNGSEGRVSSGYSINGILGIQHANDVNVNSMKRKRVDDHDENRDINIHMEE
DIKRQRIQYNGDQIYPNLWSSKWCVKDEPKHQDLVNSVVVAMPTPPHNNNNSSANNNNNS
NSNNNTSSNNNNNNPSANNNTSSYYDTHNVFPTSVNNNNNQDTILYDSITTISQAQNTLY
APSIGTAIGTGTFTSLAPLSMQDIKLNATTTLIDQSMSPYHADSTTPYNTLAMSQIEDGI
PQATQQDQPDSSSELPMFTMISPDGQSTSQGLIKNDTNNNNNDRNNNKSKDKLHHDDDHS
KRQLLQRYRLEDGVDHATTIHHPHHLLLLQQQQQQMNSQMGHSMDGKSNLIPVPENSPSL
IVLQPSAQSGGYSSFFNHYATANNGSVVAASDYAYNSAPYQQYSTPYNYGYNVPTTSSLL
NTTYYFNNEQTSDLRSPLAATRANSLASASSPTGACVKTEISAKDIFLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g15624.t1 | CDD | cd00131 | PAX | 20 | 146 | 2.79559E-82 |
| 10 | g15624.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 12 | 87 | 1.2E-39 |
| 9 | g15624.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 88 | 167 | 1.9E-35 |
| 17 | g15624.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 195 | - |
| 16 | g15624.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 157 | 195 | - |
| 15 | g15624.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 455 | 480 | - |
| 14 | g15624.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 465 | 480 | - |
| 2 | g15624.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 18 | 512 | 8.8E-105 |
| 3 | g15624.t1 | PANTHER | PTHR45636:SF16 | PAIRED BOX POX-MESO PROTEIN | 18 | 512 | 8.8E-105 |
| 7 | g15624.t1 | PRINTS | PR00027 | Paired box signature | 23 | 38 | 4.5E-41 |
| 6 | g15624.t1 | PRINTS | PR00027 | Paired box signature | 41 | 59 | 4.5E-41 |
| 5 | g15624.t1 | PRINTS | PR00027 | Paired box signature | 61 | 78 | 4.5E-41 |
| 4 | g15624.t1 | PRINTS | PR00027 | Paired box signature | 79 | 96 | 4.5E-41 |
| 1 | g15624.t1 | Pfam | PF00292 | ‘Paired box’ domain | 20 | 143 | 3.5E-70 |
| 13 | g15624.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 53 | 69 | - |
| 18 | g15624.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 19 | 145 | 62.885 |
| 12 | g15624.t1 | SMART | SM00351 | pax3 | 19 | 143 | 6.6E-90 |
| 8 | g15624.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 21 | 144 | 3.58E-39 |
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:0003677 | DNA binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K15608 (paired box protein 2)
Pathway
This gene does not belong to any 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