General information for g416.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 g416 is located on chr_3: 3285041..3293547 (+ 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 | g416 | g416.t1 | isoform | g416.t1 | 3285041 | 3293547 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon1 | 3285041 | 3285231 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS1 | 3285041 | 3285231 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon2 | 3285293 | 3285309 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS2 | 3285293 | 3285309 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon3 | 3285368 | 3285475 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS3 | 3285368 | 3285475 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon4 | 3285543 | 3285554 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS4 | 3285543 | 3285554 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon5 | 3286108 | 3286119 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS5 | 3286108 | 3286119 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon6 | 3286360 | 3286386 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS6 | 3286360 | 3286386 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon7 | 3286726 | 3286740 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS7 | 3286726 | 3286740 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon8 | 3286814 | 3286825 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS8 | 3286814 | 3286825 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon9 | 3286894 | 3286926 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS9 | 3286894 | 3286926 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon10 | 3287005 | 3287016 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS10 | 3287005 | 3287016 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon11 | 3287765 | 3287797 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS11 | 3287765 | 3287797 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon12 | 3288042 | 3288056 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS12 | 3288042 | 3288056 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon13 | 3288126 | 3288152 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS13 | 3288126 | 3288152 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon14 | 3291286 | 3291475 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS14 | 3291286 | 3291475 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon15 | 3291854 | 3292266 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS15 | 3291854 | 3292266 |
| chr_3 | g416 | g416.t1 | exon | g416.t1.exon16 | 3292922 | 3293547 |
| chr_3 | g416 | g416.t1 | cds | g416.t1.CDS16 | 3292922 | 3293547 |
| chr_3 | g416 | g416.t1 | TSS | g416.t1 | NA | NA |
| chr_3 | g416 | g416.t1 | TTS | g416.t1 | NA | NA |
Sequences
>g416.t1 Gene=g416 Length=1743
ATGAAGAAATTTTTTTTATTACTTTTTTGTGGATTTTTTGTTGTAGCTTTTAGTGCAAAT
ATTCCTGTGGTTAAAGAAATTGAAAATGTTGATGAATTTGTGAAGGAACCAAGTGAAAAT
GTTGAAAATATTGATTTCAAAGCTGGACTTCATCATGGATTAATTAAACAAAAAATTAAG
GATAAATTGAACAATAAATACAATAAATCTCCATCAACTTTGACATGGTCTTTCACGATT
CCGTCTTTCCCAACTTTCCCTACGACTTCTTCAACATCGTCTACGAGCACGACAACAAGC
ACCACTACGACAACTACGCCCACAACAACAACCACAACAACTCCATCTACGACAACAACA
ACAACAACTCCAACAACAACGACTACTACAACAACTACTACACCAACAACTACAACAACA
ACACCATCTACCACAACAACTACCACACCAACAACTACAACAACAACACCGACTACCACC
ACAACAACTACCACACCAGCAACAACTGCTGCAGTGGCGACCAAAGTGGATAAAAAAATT
GATTCGCCTCAATCATCACCAAAACAATTGTCATCAACTGACGACAATTCTAAAATGACA
CCAGCAGCAAGTCCGCCAGCAGCATTGCCTTCATGGGCTCCAATTTTATTTCCTCCATGG
AATGCTAGTTTATTTTATCCCGCCGCATTACGATCACTGCCAAATTTTCTTGAGAGCATG
AAGTTGCCGACAACAGTCAATAATAGCAGCATTAATACAAAACCAAGTTCAGGTTTTCAT
ATTTGTGATATTTTGGAATTGAATAAAGAAAAGAAAGAGCCAGAAATTAAACGAGATGAA
GAATTAGATGAAAAATCATGTGATGAAGATGAAGATGAAATTCAAACAGCAACAATCAAA
CGCAGACATAGTCCATCACCAAATAGTCAGCATGAAAATGAAGAAAACAATAATCAAGAA
GAAAATTCACAAGATTCAAGTAGTAAATCAAAGAAGAAACATAAAGAAAATGATCAAAAT
CAACAGCAGCAGCAAATTCTTAATGACACAATCCATCAGTACTCATCGCATTTATTTCAA
AATCATCCTGCAATGCGACCATGGTTTAATTCAAATGTTTTTCATCATCAAAATGCAGCA
ACTGCAACAGAAAATCTTTCACCAATTAATGAATTGACAGAATTATCTTATGGAAATCTT
CATTCACGTCATCATCAATCGATGCTTGAAAAGAATCGAAAATATTTTCAACATTTACAG
CAACAACTTCATCATCAGCAACAGCAGCAGCAGCAAGCAGAAATATCAGCAAGATCAGAA
TCATATCCATCAGATACAGAAGATGATCATGTAGATATTGAAGAAGATGATGAGAATGGT
GAAATTATTGAAATGGATGATGATGAACATGAACATAATCATACAGGTGATAACTCGACT
GGCACGAGTGGAATAATCAACAAGAAAAGAAAACGACGTGTGCTTTTTTCAAAGGCTCAA
ACTTTTGAACTTGAAAGACGATTTAGACAACAAAGATATTTGTCAGCACCTGAACGTGAA
CATCTTGCATCACTTATTCGTCTAACACCGACACAAGTTAAAATTTGGTTCCAAAATCAT
CGTTATAAGACAAAAAGAGCAGCTCATGAGAAAGGCATGGAACATCATCATCACGTCATC
ATCATCAGAGTGCAGCCAATAGTGGCTTACATTCACCAAGACGTGTCGCTATTCCGGTGC
TAG
>g416.t1 Gene=g416 Length=580
MKKFFLLLFCGFFVVAFSANIPVVKEIENVDEFVKEPSENVENIDFKAGLHHGLIKQKIK
DKLNNKYNKSPSTLTWSFTIPSFPTFPTTSSTSSTSTTTSTTTTTTPTTTTTTTPSTTTT
TTTPTTTTTTTTTTPTTTTTTPSTTTTTTPTTTTTTPTTTTTTTTPATTAAVATKVDKKI
DSPQSSPKQLSSTDDNSKMTPAASPPAALPSWAPILFPPWNASLFYPAALRSLPNFLESM
KLPTTVNNSSINTKPSSGFHICDILELNKEKKEPEIKRDEELDEKSCDEDEDEIQTATIK
RRHSPSPNSQHENEENNNQEENSQDSSSKSKKKHKENDQNQQQQQILNDTIHQYSSHLFQ
NHPAMRPWFNSNVFHHQNAATATENLSPINELTELSYGNLHSRHHQSMLEKNRKYFQHLQ
QQLHHQQQQQQQAEISARSESYPSDTEDDHVDIEEDDENGEIIEMDDDEHEHNHTGDNST
GTSGIINKKRKRRVLFSKAQTFELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH
RYKTKRAAHEKGMEHHHHVIIIRVQPIVAYIHQDVSLFRC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g416.t1 | CDD | cd00086 | homeodomain | 490 | 546 | 6.39666E-19 |
| 10 | g416.t1 | Gene3D | G3DSA:1.10.10.60 | - | 456 | 548 | 5.6E-23 |
| 22 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 205 | - |
| 27 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 171 | - |
| 21 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 179 | 200 | - |
| 24 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 275 | 343 | - |
| 28 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 292 | 318 | - |
| 25 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 325 | 339 | - |
| 23 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 418 | 451 | - |
| 26 | g416.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 418 | 440 | - |
| 2 | g416.t1 | PANTHER | PTHR24340:SF82 | HOMEOBOX PROTEIN VND | 248 | 556 | 1.3E-61 |
| 3 | g416.t1 | PANTHER | PTHR24340 | HOMEOBOX PROTEIN NKX | 248 | 556 | 1.3E-61 |
| 6 | g416.t1 | PRINTS | PR00024 | Homeobox signature | 511 | 522 | 8.0E-5 |
| 5 | g416.t1 | PRINTS | PR00024 | Homeobox signature | 526 | 536 | 8.0E-5 |
| 4 | g416.t1 | PRINTS | PR00024 | Homeobox signature | 536 | 545 | 8.0E-5 |
| 1 | g416.t1 | Pfam | PF00046 | Homeodomain | 490 | 546 | 7.1E-18 |
| 12 | g416.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 13 | g416.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g416.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 15 | g416.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 11 | g416.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 580 | - |
| 20 | g416.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 522 | 545 | - |
| 29 | g416.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 487 | 547 | 19.564 |
| 19 | g416.t1 | SMART | SM00389 | HOX_1 | 489 | 551 | 1.3E-21 |
| 7 | g416.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 475 | 547 | 6.42E-23 |
| 9 | g416.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 17 | g416.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 8 | g416.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 26 | - |
| 18 | g416.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 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 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.
