General information for g7963.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeobox protein invected.
Parent gene
- The parent gene g7963 is located on chr_2: 27292919..27294139 (- 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 | g7963 | g7963.t1 | isoform | g7963.t1 | 27282265 | 27294139 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon1 | 27282265 | 27282337 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS1 | 27282265 | 27282337 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon2 | 27282397 | 27282566 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS2 | 27282397 | 27282566 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon3 | 27282626 | 27282729 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS3 | 27282626 | 27282729 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon4 | 27284143 | 27284148 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS4 | 27284143 | 27284148 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon5 | 27292645 | 27292681 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS5 | 27292645 | 27292681 |
| chr_2 | g7963 | g7963.t1 | exon | g7963.t1.exon6 | 27292919 | 27294139 |
| chr_2 | g7963 | g7963.t1 | cds | g7963.t1.CDS6 | 27292919 | 27294139 |
| chr_2 | g7963 | g7963.t1 | TSS | g7963.t1 | 27294532 | 27294532 |
| chr_2 | g7963 | g7963.t1 | TTS | g7963.t1 | NA | NA |
Sequences
>g7963.t1 Gene=g7963 Length=1611
ATGATGGCCATATTTATGCCAACGGACTTTAAGAGCTTGAGTATAAACAATTTTCTTAAA
CTTCAATATCCGTCGCAAATTGCAGCTAATGAAAGTCACTTTAGATCGCATTTCAATATT
GGCGTTGTAGAGTCAGCTATGTCAAATGTTGTCAGTGGTCCATTGCCACATCAACCGCCA
ACGATGATGACCAGTGAAGTTATGAGTGATCAGAATGTGAAAGTAAGACTGTGTTCAGAA
GATGATAGTAATAGCAATGACAGTGACTTGTCAGTAGGACAAGAGAAAGTTCTCAATGAG
CAGAACGAATCGAATAATAATGTAAATGTGAAAGAACCTGTGAGTTCTGATGTTGATGAT
GAAGAGATGAGCAATGCATCATCATCACAATATACAAATAGTTCAACACGATTATGTAGT
CCACAGAACTCTAATGAGATTATGCGACCAATACATTTCCATGAAGAGATTATTAGAAGT
TCACAAATTTATGCAGAAGAACTATTGAGACAGCGAATTGCTGCTGCTGCTCGTCTTCAA
AGTGTTGCAAATGAATCAAAAAATCACAGTTTAGACGAACCTGAACCATCGATAATTTCT
AAATTAAATTTTCAATCAGGCATGTTTTCCGCAACTTCAAAACACACCGCCGACAACAGC
AGCAATGCCGAAAATGGCAGCGGGAATAATTTGTTTTGTGCCAAAAGTGCCATAAATTTT
TCAAACATTCACTCACATCTCAGTGCAATTTCCCAGATTACTCATAATCTAGGTGGCAAT
ATGAAAAAGGACGATGCAACAAGCTTAAGTAGCCTTTCGCGCGAGAGCTCACAATCGCCA
TCGGGCTTTCAACAATTTAAGCAGCGCGGTTTTCACACGGCCTCGTCCATTCATCAAAAT
CAATTTCATGATCATAGTTTAAAATTTAGTATCGATAATATATTAAAGGCTGATTTTGGT
CGTAGAATTACCGAGCCCCTGCTGAAAACATCGAGATTAAAACGAAATATTCGGGGCGAA
GGAAAGCATGAAAAAGAAAAGATCAATAAGTTTACTGACATGGAGACATTACAACAACAA
AAAGAACCTCATAATAGTACTGTGACAAAAGACAAATCTTTAGATCAATCGTATTCTTCA
TCAGCCGAAACATCAAAAGGCGATGCTGGATCAAGTAGTGCTCCCGGATCATCGAGTGGA
GGAACAGTGTGGCCAGCATGGGTATTTTGCACTCGTTATTCCGATCGACCAAGTTCAGGG
CGAAGTCCGCGAGTTAAGAAAAAAAAGGCACCCTCAGAGTCGAGCTCAAAAGATGATGAG
AAAAGACCACGCACTGCTTTCTCGGGCGCTCAATTAGCACGACTTAAACACGAGTTTAAT
GAAAATCGATATTTGACTGAAAAGCGGCGACAACAATTGAGTAGTGAGCTGGGTCTAAAT
GAGGCACAAATCAAAATTTGGTTCCAAAATAAAAGAGCAAAAATTAAGAAATCATCGGGC
ACCAAAAACCCACTTGCAATTCAACTAATGGCCCAGGGGCTTTATAATCACTCCACAGTA
CCATTATCGAAGGAAGAAGAAGAATTGCAAGAGCTTCAATCTGGAAATTGA
>g7963.t1 Gene=g7963 Length=536
MMAIFMPTDFKSLSINNFLKLQYPSQIAANESHFRSHFNIGVVESAMSNVVSGPLPHQPP
TMMTSEVMSDQNVKVRLCSEDDSNSNDSDLSVGQEKVLNEQNESNNNVNVKEPVSSDVDD
EEMSNASSSQYTNSSTRLCSPQNSNEIMRPIHFHEEIIRSSQIYAEELLRQRIAAAARLQ
SVANESKNHSLDEPEPSIISKLNFQSGMFSATSKHTADNSSNAENGSGNNLFCAKSAINF
SNIHSHLSAISQITHNLGGNMKKDDATSLSSLSRESSQSPSGFQQFKQRGFHTASSIHQN
QFHDHSLKFSIDNILKADFGRRITEPLLKTSRLKRNIRGEGKHEKEKINKFTDMETLQQQ
KEPHNSTVTKDKSLDQSYSSSAETSKGDAGSSSAPGSSSGGTVWPAWVFCTRYSDRPSSG
RSPRVKKKKAPSESSSKDDEKRPRTAFSGAQLARLKHEFNENRYLTEKRRQQLSSELGLN
EAQIKIWFQNKRAKIKKSSGTKNPLAIQLMAQGLYNHSTVPLSKEEEELQELQSGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g7963.t1 | CDD | cd00086 | homeodomain | 441 | 499 | 6.18528E-21 |
| 13 | g7963.t1 | Gene3D | G3DSA:1.10.10.60 | - | 411 | 501 | 1.6E-23 |
| 18 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 113 | - |
| 21 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 142 | - |
| 20 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 120 | 142 | - |
| 26 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 264 | 284 | - |
| 23 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 336 | 352 | - |
| 24 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 336 | 397 | - |
| 19 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 353 | 397 | - |
| 25 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 418 | 446 | - |
| 22 | g7963.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 426 | 445 | - |
| 3 | g7963.t1 | PANTHER | PTHR24341 | HOMEOBOX PROTEIN ENGRAILED | 362 | 529 | 1.0E-89 |
| 4 | g7963.t1 | PANTHER | PTHR24341:SF7 | SEGMENTATION POLARITY HOMEOBOX PROTEIN ENGRAILED | 362 | 529 | 1.0E-89 |
| 6 | g7963.t1 | PRINTS | PR00026 | Engrailed homeodomain signature | 439 | 456 | 5.2E-16 |
| 8 | g7963.t1 | PRINTS | PR00024 | Homeobox signature | 462 | 473 | 3.4E-6 |
| 11 | g7963.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 469 | 478 | 6.8E-6 |
| 9 | g7963.t1 | PRINTS | PR00024 | Homeobox signature | 477 | 487 | 3.4E-6 |
| 10 | g7963.t1 | PRINTS | PR00031 | Lambda-repressor HTH signature | 478 | 494 | 6.8E-6 |
| 7 | g7963.t1 | PRINTS | PR00024 | Homeobox signature | 487 | 496 | 3.4E-6 |
| 5 | g7963.t1 | PRINTS | PR00026 | Engrailed homeodomain signature | 502 | 519 | 5.2E-16 |
| 2 | g7963.t1 | Pfam | PF00046 | Homeodomain | 441 | 497 | 4.7E-21 |
| 1 | g7963.t1 | Pfam | PF10525 | Engrailed homeobox C-terminal signature domain | 498 | 528 | 1.3E-17 |
| 16 | g7963.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 473 | 496 | - |
| 17 | g7963.t1 | ProSitePatterns | PS00033 | ‘Homeobox’ engrailed-type protein signature. | 509 | 516 | - |
| 27 | g7963.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 438 | 498 | 21.006 |
| 15 | g7963.t1 | SMART | SM00389 | HOX_1 | 440 | 502 | 1.1E-24 |
| 12 | g7963.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 434 | 499 | 7.7E-22 |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0007275 | multicellular organism development | BP |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K09319 (homeobox protein engrailed)
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.
