General information for g2573.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein vnd.
Parent gene
- The parent gene g2573 is located on chr_3: 18812034..18814906 (- 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 | g2573 | g2573.t1 | TTS | g2573.t1 | 18811906 | 18811906 |
| chr_3 | g2573 | g2573.t1 | isoform | g2573.t1 | 18812034 | 18814906 |
| chr_3 | g2573 | g2573.t1 | exon | g2573.t1.exon1 | 18812034 | 18812776 |
| chr_3 | g2573 | g2573.t1 | cds | g2573.t1.CDS1 | 18812034 | 18812776 |
| chr_3 | g2573 | g2573.t1 | exon | g2573.t1.exon2 | 18812981 | 18813339 |
| chr_3 | g2573 | g2573.t1 | cds | g2573.t1.CDS2 | 18812981 | 18813339 |
| chr_3 | g2573 | g2573.t1 | exon | g2573.t1.exon3 | 18814785 | 18814906 |
| chr_3 | g2573 | g2573.t1 | cds | g2573.t1.CDS3 | 18814785 | 18814906 |
| chr_3 | g2573 | g2573.t1 | TSS | g2573.t1 | NA | NA |
Sequences
>g2573.t1 Gene=g2573 Length=1224
ATGTGCAGTCAACAAGTGGATAATCAACAGCAGCTACCTTCTCAAGTAGATTTTGTAAAC
GTTGATGAATATGAACCGTCATTTCAATTAATACCACCATTTGGTGAATATGACTATAAA
GAAATAATTGATAAAAATCCACAGAGATCTGGATTTCATATAAGTGATATACTTCAGTTA
AATAGTGAAGCAAATGTAGAAAATTCAAAACCACGAACATCAATTGACTACTCAATTTAT
AATTATAACGACTATCAGTCACGCCACTATTATTCTCCTTATCCGCATCCACAAATTCTT
CCATCAACTTTATCTACTTTCGAGAGTGATCTTCCATTTTACAATGCTGCATTCAATTCA
CAACCACCTTCTGTATACAATAGTAACGTTTATTTTGCATCAGACACAACAAGTAATAGT
TTTTCCGGAAATCAAATGAATCGTTATCTTGTAAATGATGCAAATAATAACAGCAGTTAT
GCATCATATTATGAGCAACAATATCATCACCATCATCATCATCACACATCTCATCAAAAT
ATAATGCCACAAACGAGTCCTGATTCAACTAGTCCACTAGTTAACACTGATTCTTCCTAT
CTCACGCTTCCTCAACCAAAAAGTTCATCATATAGTTCAAGTTCACCATCACATGAAATG
ACATCAAAAGAAACAAAGTACACAACTTTAAGTTCAATTTCACCACAAACATCGACAACA
GCAAAAAATGAAAATTTCTCAACTCATTCCACAGATCTTGATGTAGGTGGAAATAATGAT
GATCATTTGAGTATGGATGAAAGTAGTGAAAGTATCGATGAAATGCATGATGGAGCAAGT
GATAGTCAAACAACATCACAAAATTCAAGTGAGAAAAAGCGAAAACGTCGTGTGCTCTTC
ACAAAATCTCAAACATTTGAACTTGAGCGACGTTTTCGACAGCAACGATATTTATCAGCA
CCTGAAAGAGAACATCTTGCATCACTTATTGGTCTTACACCAACGCAGGTGAAGATTTGG
TTTCAAAATCATCGCTACAAGACGAAACGAGCAAGTCATGAAAAGTCACCAGGCACATCT
AATACATTTCCAACAAGACTTCCATCACCTAATGCTATAAAACGTGTTCATGTGCCTGTA
TTGATTTCTGATGGAAAACCAGTTTTAAATGATAATTTAAATTTTAATCAATCGAGTGGA
GGTCAAAAGTGGTGGCAAGTCTAA
>g2573.t1 Gene=g2573 Length=407
MCSQQVDNQQQLPSQVDFVNVDEYEPSFQLIPPFGEYDYKEIIDKNPQRSGFHISDILQL
NSEANVENSKPRTSIDYSIYNYNDYQSRHYYSPYPHPQILPSTLSTFESDLPFYNAAFNS
QPPSVYNSNVYFASDTTSNSFSGNQMNRYLVNDANNNSSYASYYEQQYHHHHHHHTSHQN
IMPQTSPDSTSPLVNTDSSYLTLPQPKSSSYSSSSPSHEMTSKETKYTTLSSISPQTSTT
AKNENFSTHSTDLDVGGNNDDHLSMDESSESIDEMHDGASDSQTTSQNSSEKKRKRRVLF
TKSQTFELERRFRQQRYLSAPEREHLASLIGLTPTQVKIWFQNHRYKTKRASHEKSPGTS
NTFPTRLPSPNAIKRVHVPVLISDGKPVLNDNLNFNQSSGGQKWWQV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g2573.t1 | CDD | cd00086 | homeodomain | 294 | 350 | 5.06078E-21 |
| 10 | g2573.t1 | Gene3D | G3DSA:1.10.10.60 | - | 265 | 352 | 1.8E-24 |
| 15 | g2573.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 167 | 296 | - |
| 16 | g2573.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 179 | 254 | - |
| 14 | g2573.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 277 | - |
| 2 | g2573.t1 | PANTHER | PTHR24340:SF82 | HOMEOBOX PROTEIN VND | 46 | 391 | 1.3E-67 |
| 3 | g2573.t1 | PANTHER | PTHR24340 | HOMEOBOX PROTEIN NKX | 46 | 391 | 1.3E-67 |
| 4 | g2573.t1 | PRINTS | PR00024 | Homeobox signature | 315 | 326 | 2.6E-5 |
| 8 | g2573.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 322 | 331 | 8.3E-5 |
| 6 | g2573.t1 | PRINTS | PR00024 | Homeobox signature | 330 | 340 | 2.6E-5 |
| 7 | g2573.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 331 | 347 | 8.3E-5 |
| 5 | g2573.t1 | PRINTS | PR00024 | Homeobox signature | 340 | 349 | 2.6E-5 |
| 1 | g2573.t1 | Pfam | PF00046 | Homeodomain | 294 | 350 | 1.3E-19 |
| 13 | g2573.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 326 | 349 | - |
| 17 | g2573.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 291 | 351 | 20.018 |
| 12 | g2573.t1 | SMART | SM00389 | HOX_1 | 293 | 355 | 1.2E-23 |
| 9 | g2573.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 276 | 351 | 3.04E-24 |
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 transcript has been annotated with K08029 (homeobox protein Nkx-2.2)
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.
