General information for g8380.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Paired box protein Pax-6.
Parent gene
- The parent gene g8380 is located on chr_2: 30092871..30099725 (- 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 | g8380 | g8380.t1 | isoform | g8380.t1 | 30079820 | 30098482 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon1 | 30079820 | 30079890 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS1 | 30079820 | 30079890 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon2 | 30080200 | 30080693 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS2 | 30080200 | 30080693 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon3 | 30080766 | 30081203 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS3 | 30080766 | 30081203 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon4 | 30081266 | 30081343 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS4 | 30081266 | 30081343 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon5 | 30081401 | 30081587 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS5 | 30081401 | 30081587 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon6 | 30086124 | 30086547 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS6 | 30086124 | 30086547 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon7 | 30092731 | 30092799 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS7 | 30092731 | 30092799 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon8 | 30092871 | 30092982 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS8 | 30092871 | 30092982 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon9 | 30093049 | 30093211 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS9 | 30093049 | 30093211 |
| chr_2 | g8380 | g8380.t1 | exon | g8380.t1.exon10 | 30098413 | 30098482 |
| chr_2 | g8380 | g8380.t1 | cds | g8380.t1.CDS10 | 30098413 | 30098482 |
| chr_2 | g8380 | g8380.t1 | TSS | g8380.t1 | NA | NA |
| chr_2 | g8380 | g8380.t1 | TTS | g8380.t1 | NA | NA |
Sequences
>g8380.t1 Gene=g8380 Length=2106
ATGGGCGCATCGCCCTGGTCTTCAACGATGATGATGGATCGCATATCACTCGATGATATG
CCTCATAAAGGATCGGGAGTAAATCAATTAGGCGGAATCTTTGTAGGTGGCCGACCATTG
CCGGACTCAACGAGACAGAAGATTGTTGAACTGGCGCATTCGGGTGCTCGACCTTGCGAT
ATATCTAGAATCTTGCAAGTCTCCAATGGCTGCGTTAGCAAAATTTTAGGAAGATATTAT
GAAACTGGTAGTATAAGGCCAAGAGCGATTGGCGGTTCAAAACCAAGAGTTGCAACAACT
GAAGTTGTTAATAAAATTTCACACTACAAGCGTGAATGTCCTTCGATCTTTGCATGGGAA
ATTCGTGATCGACTGTTGCAAGAAGGAGTGTGCTCTAATGATAACATACCAAGTGTGTCT
TCAATAAATCGTGTTTTGAGGAATTTGGCGGCACAAAAAGAGCAACAGCAGCAACAGAGT
CACACAACAACGCCATCAAATAGCGTTCCAATTAATAGCTATCAACCAACATCGCTTGTT
AATGACACAATTTATGATAAGCTACGTTTATTGAACAACAATCATCGCCATCAATCAATT
CGTGACTCTTGTTGGCCTCCTCGAAGCCCAACTACAGCATCTTGGTATCCACATTTAAAT
TCGCACCATCAACAAGAAGCAAACATTAATGCAAATGACACAGCAACAAATCCATTGACA
ACAAGCATCATGTCGCCTCAATCCACTACTCCGATAAAAGAATATTCATCATTGAGTCCC
AATTCATGTAAAGCTTCATCGATTAATGATGATTTGACAAAAACTGCTTCAAAGAAAGAA
ACCCAATCAGATGGAAATATTTCTGGTGGTGAGGGTGAAAATTCAAACACCGATTCAACA
ATTGACACCGATGACGATCAAGCGAGATTGAGGCTAAAGAGAAAATTGCAACGTAATCGT
ACTTCATTTTCCAATGATCAAATCGACAGCTTGGAAAAGGAATTTGAAAGAACACATTAT
CCTGATGTTTTTGCTAGAGAACGTCTTGCTGTTAAAATTGGCTTACCAGAAGCTCGCATT
CAAGTGTGGTTTTCTAATCGAAGAGCAAAATGGCGACGGGAAGAAAAACTTCGAACGCAA
CGTTTAACAACCCCGAATAATAGCAACAACAACAATTCATTGAATGTCAATAATAATAAT
ACAAATAATAATAATAATGAAATCAGCTGTGCCAATGACACAAATTCATCAACTGATACA
AATCCCAAGGTGAATGTTAATAATGATTCGTCGAGCATCAATAGTATGTTGCATAATTCG
CATGTTGGAGGTAATATTACTGATGCACATAATTCTGGTATTATTGGGGATATGCATAAT
TCACTGATGAATGGTAATCATCATTTATCAACTCCATCGAGCTTAATTACGCCAACTTCA
GCACCGTCACTTTCGCCACCACGTTTTAATTTTAATCATGGCTTCTGTAGCACAATGAGC
CCGATGTATACGCCACAAATGTCTATTTCTGATTCTTATAGTTCAATGCCATTTTCACAT
GCACCAATAAGTTCAATGGCAAGTTTATCATCTAATCCATTAGGAATACAACAGCAACAA
CATGTACAGCACAAATACGAGCAACATCAGCATCAACAATATCATCAACGTACTGAGGAT
ATGACTCCACCCTCTACATATCAATGTCACATGTCGCGATTGAATATTCCATCGCCCTCA
CTGCAATCTTTGCATCAAGCATCACACTCGGGATTATCTTCACTTCAAAATCATCATACG
TACTCATCAAGTTCATCATCCCCTCATAGTGCACCATTAGATGCCACTCAAGCGTCACAT
TCACATTCAATTCCTCCCGCAACTAGTCCTCCATCATCATTAGCTCCGCCAAGCTCTATT
TATTCATATGATCCTATCAATATCGGTTATCCATCAACAAGATTATCACCATGCAATTCA
AATGATAATTATCAACTTAATGGAGGCTCTTATGGAAATACTAATGGAAGTTCGGGCTTA
ATATCATCATTACATAATCCATCATCATCAGCAGATATGGCTCATTACTTTCTTAGACTT
CAATGA
>g8380.t1 Gene=g8380 Length=701
MGASPWSSTMMMDRISLDDMPHKGSGVNQLGGIFVGGRPLPDSTRQKIVELAHSGARPCD
ISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATTEVVNKISHYKRECPSIFAWE
IRDRLLQEGVCSNDNIPSVSSINRVLRNLAAQKEQQQQQSHTTTPSNSVPINSYQPTSLV
NDTIYDKLRLLNNNHRHQSIRDSCWPPRSPTTASWYPHLNSHHQQEANINANDTATNPLT
TSIMSPQSTTPIKEYSSLSPNSCKASSINDDLTKTASKKETQSDGNISGGEGENSNTDST
IDTDDDQARLRLKRKLQRNRTSFSNDQIDSLEKEFERTHYPDVFARERLAVKIGLPEARI
QVWFSNRRAKWRREEKLRTQRLTTPNNSNNNNSLNVNNNNTNNNNNEISCANDTNSSTDT
NPKVNVNNDSSSINSMLHNSHVGGNITDAHNSGIIGDMHNSLMNGNHHLSTPSSLITPTS
APSLSPPRFNFNHGFCSTMSPMYTPQMSISDSYSSMPFSHAPISSMASLSSNPLGIQQQQ
HVQHKYEQHQHQQYHQRTEDMTPPSTYQCHMSRLNIPSPSLQSLHQASHSGLSSLQNHHT
YSSSSSSPHSAPLDATQASHSHSIPPATSPPSSLAPPSSIYSYDPINIGYPSTRLSPCNS
NDNYQLNGGSYGNTNGSSGLISSLHNPSSSADMAHYFLRLQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g8380.t1 | CDD | cd00131 | PAX | 25 | 150 | 3.55035E-78 |
| 16 | g8380.t1 | CDD | cd00086 | homeodomain | 318 | 375 | 8.99167E-24 |
| 14 | g8380.t1 | Coils | Coil | Coil | 139 | 159 | - |
| 12 | g8380.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 16 | 91 | 3.5E-39 |
| 13 | g8380.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 92 | 170 | 6.5E-34 |
| 11 | g8380.t1 | Gene3D | G3DSA:1.10.10.60 | - | 301 | 377 | 4.4E-26 |
| 23 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 151 | 173 | - |
| 22 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 272 | - |
| 26 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 306 | - |
| 21 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 279 | 297 | - |
| 24 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 542 | 563 | - |
| 25 | g8380.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 582 | 636 | - |
| 3 | g8380.t1 | PANTHER | PTHR45636:SF5 | PAIRED BOX PROTEIN PAX-6-RELATED | 16 | 628 | 1.2E-159 |
| 4 | g8380.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 16 | 628 | 1.2E-159 |
| 6 | g8380.t1 | PRINTS | PR00027 | Paired box signature | 27 | 42 | 1.3E-40 |
| 7 | g8380.t1 | PRINTS | PR00027 | Paired box signature | 45 | 63 | 1.3E-40 |
| 8 | g8380.t1 | PRINTS | PR00027 | Paired box signature | 65 | 82 | 1.3E-40 |
| 5 | g8380.t1 | PRINTS | PR00027 | Paired box signature | 83 | 100 | 1.3E-40 |
| 2 | g8380.t1 | Pfam | PF00292 | ‘Paired box’ domain | 25 | 147 | 1.4E-68 |
| 1 | g8380.t1 | Pfam | PF00046 | Homeodomain | 318 | 373 | 1.3E-21 |
| 19 | g8380.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 57 | 73 | - |
| 20 | g8380.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 349 | 372 | - |
| 28 | g8380.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 23 | 149 | 62.243 |
| 27 | g8380.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 314 | 374 | 19.823 |
| 17 | g8380.t1 | SMART | SM00351 | pax3 | 23 | 147 | 6.4E-86 |
| 18 | g8380.t1 | SMART | SM00389 | HOX_1 | 316 | 378 | 7.3E-26 |
| 9 | g8380.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 26 | 148 | 9.86E-37 |
| 10 | g8380.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 302 | 375 | 9.41E-23 |
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:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | 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