General information for g5890.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Segmentation protein paired.
Parent gene
- The parent gene g5890 is located on chr_2: 12609727..12613877 (- 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 | g5890 | g5890.t1 | isoform | g5890.t1 | 12609727 | 12613877 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon1 | 12609727 | 12610370 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS1 | 12609727 | 12610370 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon2 | 12610431 | 12610826 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS2 | 12610431 | 12610826 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon3 | 12612007 | 12612138 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS3 | 12612007 | 12612138 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon4 | 12612197 | 12612299 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS4 | 12612197 | 12612299 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon5 | 12612359 | 12612499 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS5 | 12612359 | 12612499 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon6 | 12612560 | 12612606 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS6 | 12612560 | 12612606 |
| chr_2 | g5890 | g5890.t1 | exon | g5890.t1.exon7 | 12613811 | 12613877 |
| chr_2 | g5890 | g5890.t1 | cds | g5890.t1.CDS7 | 12613811 | 12613877 |
| chr_2 | g5890 | g5890.t1 | TSS | g5890.t1 | NA | NA |
| chr_2 | g5890 | g5890.t1 | TTS | g5890.t1 | NA | NA |
Sequences
>g5890.t1 Gene=g5890 Length=1530
ATGACAATAACAAATAATTTCTCAAGTGCCGCAATGAGACCTTGCTTTAATGGATACCCA
TTACAAGGTGATATGTCTGCAGGACAAGGAAGAGTTAATCAACTTGGTGGTGTTTTTATT
AATGGTCGTCCATTGCCTTCACATATTCGATTAAAAATAGTTGAACTAGCAGCATCTGGT
GTGCGGCCTTGTCAAATTTCTCGTCAATTGCGTGTTTCTCATGGATGTGTATCAAAAATT
CTTAATCGTTACCAAGAAACAGGATCAATTAGACCTGGAGTTATTGGCGGATCAAAACCA
AGAATTGCAACACCAGAAATTGAAAATCGTATTGAAGATTATAAAAAAGAAAATCCAGGA
ATCTTTAGTTGGGAAATAAGAGATCGTCTAATTAAAGAGGGAATTTGTGATAGATCAACT
GCTCCTTCAGTATCTGCTATCTCACGATTACTGCGTGGACGTGATGACGAAAAGAGAGCC
GCACAAAACGGCGAAAACCATGCAATGAAGCAATCGGATGGTGATTTATCGGACTGCGAC
AGTGAACCGGGAATTCCACTGAAACGAAAGCAAAGACGATCAAGAACAACATTCACTGCA
ATGCAGCTTGATGAGCTCGAACGAGCTTTTGAGCGTACACAATACCCTGACATTTATACG
CGCGAAGAGCTTGCACAACGTACAAAATTAACGGAAGCAAGAATCCAAGTATGGTTTAGT
AATCGACGCGCTCGTCTGCGTAAACAGGTCACTATTCCACCATCATCAAGTTACTCATCA
ATGGGCTCAAATCCATTGGCCTACTCAGCGTCTTCTTCTGTTTCGGGTTATTCTTTATTA
CAACCATTAACTGAGGCATCACAATTTACTTCGACACCATCTCAGATGCATGATTTTTAT
TCATCACATGTTCATCAAATGGCAAATCAAGCTCGTCAATCGCCTCCAGAATCTGTCAAT
GCACAAGCAACATCGCCAGCTATTCATAATGCAAGTTCGTCTTATTATCATCACTATCAT
TCATCATCAATTGGCTTGAGTTCAAATCAAAATAATTCTGTACCTAATGCAGCTAACTAT
TCTCCACCAACAAATCAAAATGGCACAATAAATGGAAATGAAAGTCCAAATTCAGTTGAT
CAATTTGCAAACAATCCCAGTAATAATATTCAATTGCCTGATACACCAAACAGTCTTGTT
ACAACAATGATGGGTCCAACATCAGGAAATAGCAATAGCAATGATGGTACAAATGGAATT
AATGAATCTTCGGCTTCAGAAAATGCATCAATTAATAATAACAATAATAACTACAGTCCA
TGGTGTGCTACAGCAAGTGGCCATCAACTTCCATTGTCAAATTCACCAAATCACTTGAGC
TCATATAATACAGCTCATCACAGTTCACTCTATAGTGCACACCATAATTTGTCATCGACA
CTATTGCCACATCAAAATATCTCAAGTTTCACTCATCCACATAGTGGCAAAGGTTTTAGT
ATGTCACAGCCTTTCTATTCATGGTATTAG
>g5890.t1 Gene=g5890 Length=509
MTITNNFSSAAMRPCFNGYPLQGDMSAGQGRVNQLGGVFINGRPLPSHIRLKIVELAASG
VRPCQISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEDYKKENPG
IFSWEIRDRLIKEGICDRSTAPSVSAISRLLRGRDDEKRAAQNGENHAMKQSDGDLSDCD
SEPGIPLKRKQRRSRTTFTAMQLDELERAFERTQYPDIYTREELAQRTKLTEARIQVWFS
NRRARLRKQVTIPPSSSYSSMGSNPLAYSASSSVSGYSLLQPLTEASQFTSTPSQMHDFY
SSHVHQMANQARQSPPESVNAQATSPAIHNASSSYYHHYHSSSIGLSSNQNNSVPNAANY
SPPTNQNGTINGNESPNSVDQFANNPSNNIQLPDTPNSLVTTMMGPTSGNSNSNDGTNGI
NESSASENASINNNNNNYSPWCATASGHQLPLSNSPNHLSSYNTAHHSSLYSAHHNLSST
LLPHQNISSFTHPHSGKGFSMSQPFYSWY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5890.t1 | CDD | cd00131 | PAX | 28 | 155 | 8.38447E-84 |
| 15 | g5890.t1 | CDD | cd00086 | homeodomain | 192 | 249 | 2.87413E-24 |
| 12 | g5890.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 21 | 96 | 1.6E-38 |
| 13 | g5890.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 97 | 155 | 5.5E-32 |
| 11 | g5890.t1 | Gene3D | G3DSA:1.10.10.60 | - | 179 | 251 | 1.7E-28 |
| 20 | g5890.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 155 | 194 | - |
| 21 | g5890.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 171 | 189 | - |
| 3 | g5890.t1 | PANTHER | PTHR45636:SF9 | SEGMENTATION PROTEIN PAIRED | 17 | 442 | 2.1E-148 |
| 4 | g5890.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 17 | 442 | 2.1E-148 |
| 7 | g5890.t1 | PRINTS | PR00027 | Paired box signature | 32 | 47 | 2.2E-39 |
| 8 | g5890.t1 | PRINTS | PR00027 | Paired box signature | 50 | 68 | 2.2E-39 |
| 6 | g5890.t1 | PRINTS | PR00027 | Paired box signature | 70 | 87 | 2.2E-39 |
| 5 | g5890.t1 | PRINTS | PR00027 | Paired box signature | 88 | 105 | 2.2E-39 |
| 2 | g5890.t1 | Pfam | PF00292 | ‘Paired box’ domain | 28 | 152 | 3.9E-71 |
| 1 | g5890.t1 | Pfam | PF00046 | Homeodomain | 192 | 248 | 5.7E-21 |
| 18 | g5890.t1 | ProSitePatterns | PS00034 | Paired DNA-binding domain signature. | 62 | 78 | - |
| 19 | g5890.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 224 | 247 | - |
| 23 | g5890.t1 | ProSiteProfiles | PS51057 | Paired DNA-binding domain profile. | 28 | 154 | 62.308 |
| 22 | g5890.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 189 | 249 | 21.087 |
| 16 | g5890.t1 | SMART | SM00351 | pax3 | 28 | 152 | 2.9E-85 |
| 17 | g5890.t1 | SMART | SM00389 | HOX_1 | 191 | 253 | 2.0E-25 |
| 10 | g5890.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 30 | 152 | 4.61E-41 |
| 9 | g5890.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 184 | 250 | 9.84E-26 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5890/g5890.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5890.t1.fa.iupred3.txt does not exist
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 transcript has been annotated with K09381 (paired box protein 3/7)
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