General information for g5561.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Dorsal root ganglia homeobox protein.
Parent gene
- The parent gene g5561 is located on chr_2: 10263820..10268729 (+ 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 | g5561 | g5561.t1 | isoform | g5561.t1 | 10262445 | 10268729 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon1 | 10262445 | 10262529 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS1 | 10262445 | 10262529 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon2 | 10263034 | 10263044 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS2 | 10263034 | 10263044 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon3 | 10263820 | 10263937 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS3 | 10263820 | 10263937 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon4 | 10264012 | 10264103 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS4 | 10264012 | 10264103 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon5 | 10264168 | 10264211 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS5 | 10264168 | 10264211 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon6 | 10264313 | 10264370 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS6 | 10264313 | 10264370 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon7 | 10264904 | 10264915 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS7 | 10264904 | 10264915 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon8 | 10265645 | 10265731 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS8 | 10265645 | 10265731 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon9 | 10265793 | 10265995 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS9 | 10265793 | 10265995 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon10 | 10266056 | 10266202 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS10 | 10266056 | 10266202 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon11 | 10267995 | 10268101 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS11 | 10267995 | 10268101 |
| chr_2 | g5561 | g5561.t1 | exon | g5561.t1.exon12 | 10268224 | 10268729 |
| chr_2 | g5561 | g5561.t1 | cds | g5561.t1.CDS12 | 10268224 | 10268729 |
| chr_2 | g5561 | g5561.t1 | TTS | g5561.t1 | 10269056 | 10269056 |
| chr_2 | g5561 | g5561.t1 | TSS | g5561.t1 | NA | NA |
Sequences
>g5561.t1 Gene=g5561 Length=1470
ATGCTAGTAGACTGTCTCATAATATATTTGCAATGTCGAGATGGAAAAATTGTATATTTT
GAAGAGCTAAAAATAGGGGAAGAGAACGGGAATAAGTTATCACCCGCTTCGGGACGTGGA
ATGTTTTGCTACCACTGTCCACCATCGCTTCATAGCAATGGAACACAACAGAGACTCTCA
ACATTAGAATATCCATTCGCACCAACTCATCCATACACTAGTTATTCATATCATCCTGCA
ATTCATGATGAGACATTTGTAAGAAGAAAGCAAAGAAGAAATCGTACAACTTTCACATTG
CAGCAGTTGGAAGAACTTGAGACGGCATTCGCACAGACTCATTATCCTGATGTGTTCACT
CGAGAAGATTTAGCAATGAAAATAAACTTGACTGAAGCACGAGTTCAGGTTTGGTTTCAA
AATCGAAGAGCGAAATGGCGTAAATCTGAACGACTTAAAGAAGACCAAAGAAAACGTGAT
GGCACTGATAATGCAGAATCTGACAGGCATGATGGCGATAGCCGTGATTCACTTTCACCA
AATGTTGGTGGCGATATGGACGATGATGATGGTCATAGTTCAAGTGCAGCAGCTACAAGT
CCACGAATTGAAGGAGGAGAAAATGAACGACCAACTTCAATTAATCAAGTGCAATCAAAT
TCTACATCTGGTAGCATAACAGGATCTCCATCACCTCAATCTCATACAAAGAACCACTCA
GTATCAAGTCCAACGATATCACCTCGTACAGAGTCACCAATTGAAGTAAGTGAGCCACTT
CCGAGAAATCCAAAAACCAACAATAATCAGTTGGCTGCCTCTAATCTTTCAAATCACATC
TTTGGTAACTTTGAAAGCAATTTTCGACCTATGGATAATGGACAGCAACCACCTTTATTT
CTGCCGCCACATTTAGCATCATTGGGTTCACAGTTTACGCCACCATTATTTTCTGGTTTG
AAATGTTATTCAAGTTTCTGTACATGCTGTTCAATGAATAAATCTCACATTACATCTCCT
CAATCGTCTACAGCATCAGCATGTTCATCTTTACTCTTGGACCAGAGTCTCGCAGCGCAT
GGTGTAAGCAATCAAATTGATTCCAATTTGTGTGGCGGTAGTGCTATGAACACGGATGCT
CGATCTACATCTGTTGCGGAATTAAGAAGGAAAGCGCAGGAGCATTCGGCTGCAATATTA
CATAGCTTACATGCAGTTGCAGGTCTTTCATTGCATACTGGCATGCCTCTTCATTTCCCA
CCCATCTCCTTGCATCATGCTCTCAATCGTTCCATCAAAAATGGCCATTTCGTTACAGAT
TATTCGGCTGATATGAATCTTCTTCAAAATAACAATAACAATAATAGCAACACTAATAAT
AATAATAATAATGTAATAATAGGCAAAGTAGAGAATGTAGAAAGTGTAGATAAAATGAGA
GATAACAACAATAGAAGCAATAGTGATTAA
>g5561.t1 Gene=g5561 Length=489
MLVDCLIIYLQCRDGKIVYFEELKIGEENGNKLSPASGRGMFCYHCPPSLHSNGTQQRLS
TLEYPFAPTHPYTSYSYHPAIHDETFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFT
REDLAMKINLTEARVQVWFQNRRAKWRKSERLKEDQRKRDGTDNAESDRHDGDSRDSLSP
NVGGDMDDDDGHSSSAAATSPRIEGGENERPTSINQVQSNSTSGSITGSPSPQSHTKNHS
VSSPTISPRTESPIEVSEPLPRNPKTNNNQLAASNLSNHIFGNFESNFRPMDNGQQPPLF
LPPHLASLGSQFTPPLFSGLKCYSSFCTCCSMNKSHITSPQSSTASACSSLLLDQSLAAH
GVSNQIDSNLCGGSAMNTDARSTSVAELRRKAQEHSAAILHSLHAVAGLSLHTGMPLHFP
PISLHHALNRSIKNGHFVTDYSADMNLLQNNNNNNSNTNNNNNNVIIGKVENVESVDKMR
DNNNRSNSD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5561.t1 | CDD | cd00086 | homeodomain | 92 | 150 | 1.72832E-25 |
| 6 | g5561.t1 | Gene3D | G3DSA:1.10.10.60 | - | 82 | 152 | 1.6E-30 |
| 10 | g5561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 264 | - |
| 11 | g5561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 176 | - |
| 12 | g5561.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 209 | 252 | - |
| 3 | g5561.t1 | PANTHER | PTHR24329 | HOMEOBOX PROTEIN ARISTALESS | 37 | 402 | 1.7E-62 |
| 4 | g5561.t1 | PANTHER | PTHR24329:SF543 | DORSAL ROOT GANGLIA HOMEOBOX | 37 | 402 | 1.7E-62 |
| 2 | g5561.t1 | Pfam | PF00046 | Homeodomain | 92 | 148 | 7.0E-24 |
| 1 | g5561.t1 | Pfam | PF03826 | OAR motif | 379 | 397 | 3.1E-7 |
| 8 | g5561.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 124 | 147 | - |
| 14 | g5561.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 89 | 149 | 20.973 |
| 13 | g5561.t1 | ProSiteProfiles | PS50803 | OAR domain profile. | 383 | 396 | 11.082 |
| 9 | g5561.t1 | SMART | SM00389 | HOX_1 | 91 | 153 | 1.8E-27 |
| 5 | g5561.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 70 | 150 | 5.13E-26 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5561/g5561.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5561.t1.fa.iupred3.txt does not exist
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 K24895 (dorsal root ganglia homeobox protein)
Pathway
This gene does not belong to any 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