General information for g81.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Paired box protein Pax-6 .
Parent gene
- The parent gene g81 is located on chr_3: 746548..753215 (+ 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_3 | g81 | g81.t1 | isoform | g81.t1 | 746548 | 753215 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon1 | 746548 | 746634 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS1 | 746548 | 746634 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon2 | 750786 | 750796 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS2 | 750786 | 750796 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon3 | 750872 | 750960 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS3 | 750872 | 750960 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon4 | 751083 | 751165 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS4 | 751083 | 751165 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon5 | 752501 | 752802 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS5 | 752501 | 752802 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon6 | 752863 | 753062 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS6 | 752863 | 753062 |
| chr_3 | g81 | g81.t1 | exon | g81.t1.exon7 | 753124 | 753215 |
| chr_3 | g81 | g81.t1 | cds | g81.t1.CDS7 | 753124 | 753215 |
| chr_3 | g81 | g81.t1 | TSS | g81.t1 | NA | NA |
| chr_3 | g81 | g81.t1 | TTS | g81.t1 | NA | NA |
Sequences
>g81.t1 Gene=g81 Length=864
ATGCTGCACCACACACATCTTTCACTACCTCCAACACCACATCACAAGCTTAGCGGGCAA
TTGACTCGTGAAGAATTACAAAACGTGATCTGTTTTCGAATTCACAAATGCGTTTACGAC
TTAAAAGAAAATTACAACGAAAATCGTACATCTTTTACAAATGAACAAATTGATAGTCTT
GAAAAAGAATTCGAGAGAACGCACTATCCTGATGTATTTGCAAGAGAACGATTAGCCGAG
AAAATAGGATTACCCGAGGCAAGAATACAGGTTTGGTTTTCAAACAGGCGCGCAAAATGG
CGAAGAGAAGAGAAGCTTCGTACACAGAGACGTTCAGTTGATCATGTAAGCGGTAATGGT
GGCAGTGGAGGTGGAAATGGAAATTCAAATAATAATAACAACAATAATTCTGCTAATGGA
AATAACGGCAGTAATGGCAGCGCAAATGTAGGAAATACAAACTCAGTTAGTCCACCAGTG
CCAACAACTCCAAGAATACCTTTAAATACTGGCTTCAATTCTATGTATGCATCAATTCCA
CAACCTATAGCTACAATGGCTGAAAATTATAGTGCAATGCCACCTTCATTGGGCTCAATG
ACATCGACATGCTTGCAACAACGCGATGCATACCCATACATGTTTACAGATCCCTTACAT
TCACTTAGCAGTCCATATACATCACATTCATCGCGTTCAAGCTGCACACCAACAGCCGCA
CATCAACAACCGCCATCACAACATTACACTTCAAATGGTGGCTCAAGTACAGGTGTCATA
ACAGCTGGCGTAAGTGTTCCAGTACAAATTGGTTCACAAGACAGTTCTGGACTTGGAACA
AATTATTGGCCAAGGCTTCAGTGA
>g81.t1 Gene=g81 Length=287
MLHHTHLSLPPTPHHKLSGQLTREELQNVICFRIHKCVYDLKENYNENRTSFTNEQIDSL
EKEFERTHYPDVFARERLAEKIGLPEARIQVWFSNRRAKWRREEKLRTQRRSVDHVSGNG
GSGGGNGNSNNNNNNNSANGNNGSNGSANVGNTNSVSPPVPTTPRIPLNTGFNSMYASIP
QPIATMAENYSAMPPSLGSMTSTCLQQRDAYPYMFTDPLHSLSSPYTSHSSRSSCTPTAA
HQQPPSQHYTSNGGSSTGVITAGVSVPVQIGSQDSSGLGTNYWPRLQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g81.t1 | CDD | cd00086 | homeodomain | 49 | 104 | 3.51215E-24 |
| 5 | g81.t1 | Gene3D | G3DSA:1.10.10.60 | - | 35 | 115 | 6.0E-27 |
| 10 | g81.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 101 | 129 | - |
| 11 | g81.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 113 | 129 | - |
| 9 | g81.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 224 | 253 | - |
| 2 | g81.t1 | PANTHER | PTHR45636 | PAIRED BOX PROTEIN PAX-6-RELATED-RELATED | 40 | 287 | 1.2E-67 |
| 3 | g81.t1 | PANTHER | PTHR45636:SF29 | GH14454P | 40 | 287 | 1.2E-67 |
| 1 | g81.t1 | Pfam | PF00046 | Homeodomain | 48 | 102 | 1.4E-22 |
| 7 | g81.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 78 | 101 | - |
| 12 | g81.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 43 | 103 | 19.742 |
| 8 | g81.t1 | SMART | SM00389 | HOX_1 | 45 | 107 | 6.8E-24 |
| 4 | g81.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 45 | 106 | 8.98E-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