General information for g4928.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein nubbin.
Parent gene
- The parent gene g4928 is located on chr_2: 6034582..6036956 (- 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 | g4928 | g4928.t1 | isoform | g4928.t1 | 6016819 | 6035410 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon1 | 6016819 | 6017179 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS1 | 6016819 | 6017179 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon2 | 6017230 | 6018131 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS2 | 6017230 | 6018131 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon3 | 6018506 | 6018621 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS3 | 6018506 | 6018621 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon4 | 6019712 | 6019750 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS4 | 6019712 | 6019750 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon5 | 6027043 | 6027582 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS5 | 6027043 | 6027582 |
| chr_2 | g4928 | g4928.t1 | exon | g4928.t1.exon6 | 6035200 | 6035410 |
| chr_2 | g4928 | g4928.t1 | cds | g4928.t1.CDS6 | 6035200 | 6035410 |
| chr_2 | g4928 | g4928.t1 | TSS | g4928.t1 | NA | NA |
| chr_2 | g4928 | g4928.t1 | TTS | g4928.t1 | NA | NA |
Sequences
>g4928.t1 Gene=g4928 Length=2169
ATGCCAATACTGATGGTGGCACAAAGTGCAATAAAAAACTTGAACAATATTTGTGAACGT
AGTGATATAACTAGCGACCAACCATTGGACTTTACCATGTCGAAATTTAAACCTTCTTCA
CCAATGCGACATCCTTTTTATCAACAATTTTTTGGCAACAACAATAGCAATGATATTGCT
GCAACCGACCGGAATGAATATGAGGAACAAGGAAGGACATTGTCAGATAATGAAATGTTG
GCGTGGCGACAATTACAATTAAATGCGGAGCAGCAGAAGCAGCTAATGCTCTCCACACCT
CAAATGTCATCAACACTAAGCAATAGTGGCAATAGCTTATTGACACTTCAAGACATGATG
ATGTTGAAGCACCAGCAGAGCTTTATTAAGCGACGATTAAGCGAAGATGATTTGGATAGT
GACAATAAGATGCCAAAATTAACTCCCATTAACACTCTGCCATTATCATTAGCAAGTATG
CCACTAATGGTCGATTTGAAGTCATCACCTTATTATGGCGGTGGTGATTCACAATCGAGT
GATACAGCTGCAACTGCTTTTGGAGCATTTAGTGGTAGCAGCATGAGTCATAGAGAAAAA
TTACAAAATCAACAATACCTCGATCGTTTACGGCGTATGAATGAGCGCGGTAAAGAAAGA
ATGGCTCGCAGTCGCGTGAATTTTGAACCGAGTAATGTGGCTAAAACAGTTCGCGAGGAA
TTGGCATCTCGAAAGCAGCAAGCCAAAAAAGACGTTTCATTGAGTCGATTATCACCTGCA
CCTTCTCACGATGACGGCAGTAATCAATCAGCTGGCAGTCGAGAGAATTCAAATTTCAGT
CCACCATTGAAATTATCGACGAATCAAACAAATCAGCATAAATTTCAATCATCTGCATTA
AATCTGATCACTGATTCAGCACGGCACACTCCATCGCCGCCTGCATCGATTAACAGCAAT
TCTGCAGCAAATCAAATGGCATTTGCGGCACTTCAAAGCCAGTTACCATTGGCGCCGCTT
TTACTACAAAATCAGTTAGGCATGGGTCCCTTTGGGAATATTTCTCCTGATGATATGCAT
TCGCTACAACAAGCATTACAAGCACAACAAGCTCAATTTCATCAGCAACTTCAGAACTTC
ATGCTGCTCCAAGCGAGTGCTAATTCTGGTAATTCACAGCAAGCACAAGCTGCTGCTCAA
CTTTTAATTCAAAGTCAAGTTCAACAAGCAATGGCACAAGCTGCACAACAATTGCAAGCA
TTGCAAAAACAACAGCAAGAAGAAATAAATAATAAAATTTATAGAATGCAAGAAGAAACA
CGTGTTAAAAGTCCACCAAATAGTCCACCTCAGAGTCCACCATTAAATTATCAGAACACA
CCGAAAACCTCATTTTCTACTAATAATAATAATCAAATTACACCACCAAATTCAAATACT
GCTACAGCTCAGATATCTGCTGGCATTTTAACACCTTCAACACCAAGTTCTGGGACATTA
ACACCTCAAATGAAAAAAACTTCAAATGCAAACACAGTTAGATCAATGGAACCATCACCA
GAAGAGACAACTGATCTAGAAGAACTTGAGCAATTTGCAAAAACATTTAAACAACGAAGA
ATAAAGCTTGGCTTTACACAAGGCGATGTAGGTTTAGCAATGGGCAAACTTTATGGCAAC
GACTTTTCACAAACAACCATATCACGCTTTGAGGCATTAAACCTGAGCTTCAAAAATATG
TGCAAGCTGAAACCTTTACTTCAAAAGTGGCTGCTTGATGCCGATGGCAGTCTTGCTGGT
AATCCGGGTAGTTATGATTCTTACAGTCTATTCGGCACGAACAACATCAGTCAACTATCG
ACGCCCGATGCCATGGGTCGAAAACGTAAGAAGCGTACATCGATTGAAACAAATGTTCGG
GTATCGTTGGAACGAGCATTCATAATGAATCCAAAACCCACGAGTGAAGAGATCAGTGCA
TTGGCCGAGAATCTTTGTATGGAGAAAGAGGTCGTTCGTGTTTGGTATTGTAATCGGCGA
CAAAAAGAAAAGCGAATTAATCCAGCAGAGTCTGATAGTCCAACCGATTCTTTAAGCAGT
TCAGGTGGATTGTTTGGCATCAGTTCTTTATCACCTCACTTTTCACCGACAAATGTGAAA
CTCGAATGA
>g4928.t1 Gene=g4928 Length=722
MPILMVAQSAIKNLNNICERSDITSDQPLDFTMSKFKPSSPMRHPFYQQFFGNNNSNDIA
ATDRNEYEEQGRTLSDNEMLAWRQLQLNAEQQKQLMLSTPQMSSTLSNSGNSLLTLQDMM
MLKHQQSFIKRRLSEDDLDSDNKMPKLTPINTLPLSLASMPLMVDLKSSPYYGGGDSQSS
DTAATAFGAFSGSSMSHREKLQNQQYLDRLRRMNERGKERMARSRVNFEPSNVAKTVREE
LASRKQQAKKDVSLSRLSPAPSHDDGSNQSAGSRENSNFSPPLKLSTNQTNQHKFQSSAL
NLITDSARHTPSPPASINSNSAANQMAFAALQSQLPLAPLLLQNQLGMGPFGNISPDDMH
SLQQALQAQQAQFHQQLQNFMLLQASANSGNSQQAQAAAQLLIQSQVQQAMAQAAQQLQA
LQKQQQEEINNKIYRMQEETRVKSPPNSPPQSPPLNYQNTPKTSFSTNNNNQITPPNSNT
ATAQISAGILTPSTPSSGTLTPQMKKTSNANTVRSMEPSPEETTDLEELEQFAKTFKQRR
IKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLLDADGSLAG
NPGSYDSYSLFGTNNISQLSTPDAMGRKRKKRTSIETNVRVSLERAFIMNPKPTSEEISA
LAENLCMEKEVVRVWYCNRRQKEKRINPAESDSPTDSLSSSGGLFGISSLSPHFSPTNVK
LE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g4928.t1 | CDD | cd00086 | homeodomain | 629 | 685 | 4.68908E-12 |
| 15 | g4928.t1 | Coils | Coil | Coil | 404 | 431 | - |
| 14 | g4928.t1 | Coils | Coil | Coil | 718 | 722 | - |
| 13 | g4928.t1 | Gene3D | G3DSA:1.10.260.40 | - | 525 | 595 | 2.0E-39 |
| 12 | g4928.t1 | Gene3D | G3DSA:1.10.10.60 | - | 613 | 678 | 1.4E-22 |
| 23 | g4928.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 239 | 279 | - |
| 22 | g4928.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 260 | 279 | - |
| 24 | g4928.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 492 | 526 | - |
| 25 | g4928.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 492 | 519 | - |
| 3 | g4928.t1 | PANTHER | PTHR11636 | POU DOMAIN | 56 | 691 | 2.2E-124 |
| 4 | g4928.t1 | PANTHER | PTHR11636:SF76 | POU DOMAIN PROTEIN 2, ISOFORM B-RELATED | 56 | 691 | 2.2E-124 |
| 5 | g4928.t1 | PRINTS | PR00028 | POU domain signature | 540 | 557 | 3.1E-39 |
| 8 | g4928.t1 | PRINTS | PR00028 | POU domain signature | 563 | 576 | 3.1E-39 |
| 9 | g4928.t1 | PRINTS | PR00028 | POU domain signature | 579 | 594 | 3.1E-39 |
| 6 | g4928.t1 | PRINTS | PR00028 | POU domain signature | 627 | 647 | 3.1E-39 |
| 7 | g4928.t1 | PRINTS | PR00028 | POU domain signature | 662 | 677 | 3.1E-39 |
| 1 | g4928.t1 | Pfam | PF00157 | Pou domain - N-terminal to homeobox domain | 525 | 595 | 6.2E-37 |
| 2 | g4928.t1 | Pfam | PF00046 | Homeodomain | 629 | 685 | 5.8E-16 |
| 20 | g4928.t1 | ProSitePatterns | PS00035 | POU-specific (POUs) domain signature 1. | 539 | 551 | - |
| 21 | g4928.t1 | ProSitePatterns | PS00465 | POU-specific (POUs) domain signature 2. | 563 | 576 | - |
| 19 | g4928.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 661 | 684 | - |
| 26 | g4928.t1 | ProSiteProfiles | PS51179 | POU-specific (POUs) domain profile. | 521 | 595 | 56.458 |
| 27 | g4928.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 626 | 686 | 16.066 |
| 17 | g4928.t1 | SMART | SM00352 | pou | 521 | 595 | 9.6E-52 |
| 18 | g4928.t1 | SMART | SM00389 | HOX_1 | 628 | 690 | 2.4E-14 |
| 10 | g4928.t1 | SUPERFAMILY | SSF47413 | lambda repressor-like DNA-binding domains | 521 | 594 | 2.41E-29 |
| 11 | g4928.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 622 | 691 | 1.75E-16 |
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