General information for g4930.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein nubbin.
Parent gene
- The parent gene g4930 is located on chr_2: 6047429..6067396 (- 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 | g4930 | g4930.t1 | TTS | g4930.t1 | 6047061 | 6047061 |
| chr_2 | g4930 | g4930.t1 | isoform | g4930.t1 | 6047429 | 6067396 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon1 | 6047429 | 6047753 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS1 | 6047429 | 6047753 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon2 | 6047815 | 6048668 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS2 | 6047815 | 6048668 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon3 | 6048728 | 6048822 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS3 | 6048728 | 6048822 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon4 | 6050599 | 6050649 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS4 | 6050599 | 6050649 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon5 | 6054890 | 6055417 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS5 | 6054890 | 6055417 |
| chr_2 | g4930 | g4930.t1 | exon | g4930.t1.exon6 | 6067204 | 6067396 |
| chr_2 | g4930 | g4930.t1 | cds | g4930.t1.CDS6 | 6067204 | 6067396 |
| chr_2 | g4930 | g4930.t1 | TSS | g4930.t1 | NA | NA |
Sequences
>g4930.t1 Gene=g4930 Length=2046
ATGCCGCTTCTGGTTACACAAAGAAGAGACAGAAGCTTTATTGCGGCTGGTGAATATCAG
AAACTCTATGGCAAATTTCTTCATAATCAATATCCATTAGACATGTCCAAGTGCAAAGAT
CTTTTCGCAAATGGAAGAAATGATGATACAGTAGAGAAGGAGGAATCGGAAGATAAGAGG
CATGACGATGAAGTAACAGCAGACAAATATCACAATGAAATGACACGTCAGCTTCCGGTG
ATGCAATTACAATCGTTTAGCTATCCAAAGAATGTTTCAACGCTTTCAAGTCCTTCTTTA
ACGACGACGACAACGACATCGTCGCTAATTAATAATAATAGCCTGTTGACATTTCGAGAC
ATAATGATGCATCATCAATATCAGCAACATCAACAATTACAGAATCAGGAGCGGCATCAA
AAGACAACAACTGAAGTTGTGAATGAACCTGCAACCATATCAACTCCATCATCATCATCA
TTATCACCAAATACATCAGCAAAATTCTCACCAAAGCGCAACTATGCAGCTGAAAAGAAT
GAAATGATGCTTCATCCATTGTCCATCAATAAAACAACAACAGAGACATGTGAGAATGGC
AGTAAAATTAGTATTAATCGCTCCATACTGAATAAGGCTGAAACTCATCATCATCAAAAT
AGCTGTGCAAAGACGGTGCGCGAGGAACTTGAAGAGAGTCGGAATAAAATTCCAATGTTG
AATATTCCACTAAATCGTTCATCAAAATCACCATCACCAAGTCGTTCACATGACGGCGAA
AGTACTGATGAAGGAAGTTATCGAGAAAATTCAAACTCAAGTCCGCCACCACATTCAAAA
GATGATCATATGAGACCACTTAATTTGATCACAGATTCACGGCAATCACCATCGCCACCT
TTATCAAATAGTGCAGCAAATACAATGAATAGTATGGCAGCATTGGCAGCACTACAAACA
CAATTACCATTGGCTCCTCTTTTTTTACAAAATCAACTTGGTATGAGTGCACTTACTGGT
TTGCCTCCCACTGGGGATCTAAATGCCCTTCAACAAGCATTGCAAGCACAACAAGCTCAA
TTTCAACAACAACTTCAAAATTATATGCTGCTTCAGGCAAGCGCAAATCATACTCAACCA
ACACAAGCTGCTGCTGCACAACTTCTTATACAGAGTCAAGTTCAACAAGCAATGGCACAA
GCAGCACAACAATTGCAAGCATTGCAAAAACAGCAGCAAAATAATCTTAAAAGAACTCAT
TCACAAAGCGAAACGAACATTATGTCAAGAAGTCCATTGCATACACCCGAAAGTCCATTA
TTGGGTAGTAATAATAGAACGACACCGCCAAATTCAAATACTGCACAATTATCAGCAGCT
GGGGGCATTTTAACTCCTTCAACTCCAAATTCTGGCACTCATCCACCACAGAAAACTTTA
ACCACTGCCGCTCGTACAATGGAAGCATCGTTGGAAGAAACAACTGATTTAGAAGAACTC
GAGCAGTTCTCAAAGACATTCAAGCAGCGAAGAATAAAACTTGGCTTTACACAAGGCGAT
GTAGGTTTAGCAATGGGCAAACTTTATGGCAACGACTTTTCACAAACAACCATATCACGC
TTTGAGGCATTAAACCTGAGCTTCAAAAATATGTGCAAGCTAAAACCACTACTGCAAAAA
TGGCTCGAAGATGCTGATCGTAGTATGAATAATCCAGGAGGAATGTTTGGACCAAGTACA
TTGAGTAGTCCATTATCAACACCAGAAAATATGGGTCGTCGTCGTAAAAAGCGTACATCA
ATTGAAACTTCAGTTCGTACAGCATTAGAAAAAGCATTTTTCATAAATTCAAAACCAACA
AGTCAAGAAATTGGAAATCTGGCCGAAAACTTGTGCATTGACAAGGAAGTTGTGCGTGTG
TGGTTCTGCAATCGAAGACAAAAAGAGAAACGAACGCATCCGGGAATGAATCCAGAAAGT
CCCGAAGACTCGTTAGGTAACGGTTCAAGCATGTTTGATTTCTCATCAACAATGAAGCAG
GAATGA
>g4930.t1 Gene=g4930 Length=681
MPLLVTQRRDRSFIAAGEYQKLYGKFLHNQYPLDMSKCKDLFANGRNDDTVEKEESEDKR
HDDEVTADKYHNEMTRQLPVMQLQSFSYPKNVSTLSSPSLTTTTTTSSLINNNSLLTFRD
IMMHHQYQQHQQLQNQERHQKTTTEVVNEPATISTPSSSSLSPNTSAKFSPKRNYAAEKN
EMMLHPLSINKTTTETCENGSKISINRSILNKAETHHHQNSCAKTVREELEESRNKIPML
NIPLNRSSKSPSPSRSHDGESTDEGSYRENSNSSPPPHSKDDHMRPLNLITDSRQSPSPP
LSNSAANTMNSMAALAALQTQLPLAPLFLQNQLGMSALTGLPPTGDLNALQQALQAQQAQ
FQQQLQNYMLLQASANHTQPTQAAAAQLLIQSQVQQAMAQAAQQLQALQKQQQNNLKRTH
SQSETNIMSRSPLHTPESPLLGSNNRTTPPNSNTAQLSAAGGILTPSTPNSGTHPPQKTL
TTAARTMEASLEETTDLEELEQFSKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISR
FEALNLSFKNMCKLKPLLQKWLEDADRSMNNPGGMFGPSTLSSPLSTPENMGRRRKKRTS
IETSVRTALEKAFFINSKPTSQEIGNLAENLCIDKEVVRVWFCNRRQKEKRTHPGMNPES
PEDSLGNGSSMFDFSSTMKQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4930.t1 | CDD | cd00086 | homeodomain | 595 | 653 | 7.02167E-14 |
| 15 | g4930.t1 | Coils | Coil | Coil | 347 | 367 | - |
| 14 | g4930.t1 | Coils | Coil | Coil | 391 | 422 | - |
| 13 | g4930.t1 | Gene3D | G3DSA:1.10.260.40 | - | 496 | 566 | 1.4E-39 |
| 12 | g4930.t1 | Gene3D | G3DSA:1.10.10.60 | - | 597 | 644 | 1.6E-20 |
| 25 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 149 | 171 | - |
| 23 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 214 | 282 | - |
| 28 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 214 | 235 | - |
| 22 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 255 | - |
| 26 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 411 | 436 | - |
| 27 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 576 | 601 | - |
| 24 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 649 | 681 | - |
| 29 | g4930.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 662 | 681 | - |
| 3 | g4930.t1 | PANTHER | PTHR11636 | POU DOMAIN | 49 | 657 | 8.7E-127 |
| 4 | g4930.t1 | PANTHER | PTHR11636:SF76 | POU DOMAIN PROTEIN 2, ISOFORM B-RELATED | 49 | 657 | 8.7E-127 |
| 5 | g4930.t1 | PRINTS | PR00028 | POU domain signature | 511 | 528 | 2.0E-40 |
| 9 | g4930.t1 | PRINTS | PR00028 | POU domain signature | 534 | 547 | 2.0E-40 |
| 7 | g4930.t1 | PRINTS | PR00028 | POU domain signature | 550 | 565 | 2.0E-40 |
| 6 | g4930.t1 | PRINTS | PR00028 | POU domain signature | 593 | 613 | 2.0E-40 |
| 8 | g4930.t1 | PRINTS | PR00028 | POU domain signature | 628 | 643 | 2.0E-40 |
| 1 | g4930.t1 | Pfam | PF00157 | Pou domain - N-terminal to homeobox domain | 496 | 566 | 2.0E-37 |
| 2 | g4930.t1 | Pfam | PF00046 | Homeodomain | 595 | 651 | 2.2E-16 |
| 20 | g4930.t1 | ProSitePatterns | PS00035 | POU-specific (POUs) domain signature 1. | 510 | 522 | - |
| 21 | g4930.t1 | ProSitePatterns | PS00465 | POU-specific (POUs) domain signature 2. | 534 | 547 | - |
| 19 | g4930.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 627 | 650 | - |
| 30 | g4930.t1 | ProSiteProfiles | PS51179 | POU-specific (POUs) domain profile. | 492 | 566 | 56.955 |
| 31 | g4930.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 592 | 652 | 16.536 |
| 17 | g4930.t1 | SMART | SM00352 | pou | 492 | 566 | 6.1E-52 |
| 18 | g4930.t1 | SMART | SM00389 | HOX_1 | 594 | 656 | 5.9E-16 |
| 10 | g4930.t1 | SUPERFAMILY | SSF47413 | lambda repressor-like DNA-binding domains | 492 | 566 | 3.83E-29 |
| 11 | g4930.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 588 | 653 | 3.89E-17 |
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 |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K09364 (POU domain transcription factor, class 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. There were no conditions that were differentially expressed