General information for g779.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear hormone receptor HR96.
Parent gene
- The parent gene g779 is located on chr_3: 5978073..5979641 (- 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 | g779 | g779.t1 | TTS | g779.t1 | 5977227 | 5977227 |
| chr_3 | g779 | g779.t1 | isoform | g779.t1 | 5977377 | 5979641 |
| chr_3 | g779 | g779.t1 | exon | g779.t1.exon1 | 5977377 | 5977456 |
| chr_3 | g779 | g779.t1 | cds | g779.t1.CDS1 | 5977377 | 5977456 |
| chr_3 | g779 | g779.t1 | exon | g779.t1.exon2 | 5977520 | 5977637 |
| chr_3 | g779 | g779.t1 | cds | g779.t1.CDS2 | 5977520 | 5977637 |
| chr_3 | g779 | g779.t1 | exon | g779.t1.exon3 | 5977736 | 5978014 |
| chr_3 | g779 | g779.t1 | cds | g779.t1.CDS3 | 5977736 | 5978014 |
| chr_3 | g779 | g779.t1 | exon | g779.t1.exon4 | 5978073 | 5979530 |
| chr_3 | g779 | g779.t1 | cds | g779.t1.CDS4 | 5978073 | 5979530 |
| chr_3 | g779 | g779.t1 | exon | g779.t1.exon5 | 5979609 | 5979641 |
| chr_3 | g779 | g779.t1 | cds | g779.t1.CDS5 | 5979609 | 5979641 |
| chr_3 | g779 | g779.t1 | TSS | g779.t1 | 5979793 | 5979793 |
Sequences
>g779.t1 Gene=g779 Length=1968
ATGAGCAGACAATCAAATGAAAAAATCTGCACGATTTGTGGAGACAAATCACTAGGGTTC
AATTTCAATGTGATAAGTTGTGAAAGCTGTAAGGCATTTTTTCGACGAAATGCAATTTCT
AATAAGAAATTTACATGCCCATTTTCTAATGCCTGTGAGATAACCGTGATAACACGACGA
TTTTGCCAAAAATGTCGATTAGAAAAGTGTTTCAAGCAAGGAATGAAAAAAGAATACATA
ATGTCAGAAGAGGATAAAGAGTTAAAGCGAATTAAAATTGAACAAAATCGCAGTAAAAGA
AAGATGAAAAAGGAGGGAACAGAAAGCAGTGAGGAGAGTAAACCTTCGAAATTGACAAAA
ATCAAAGATGAAGGTTGGTCACCATTATCGACATCATCTGTACAATCACCAGATAGTAAA
TCAGAAGATTCCATTGATCATACTACAACTCTCGATCGATTAAAAATAAGTTCCGATTCT
TCAGTGGCAGAAATTGTAAATGCTATTACAGAAATTCCAAAAGAATCTAGTCAAATAATT
CAAAATGTAATGAAAACACAACAAGAGGCATTGAGTGTCATGAGTAGAATCATTCATGAG
CCTAATCAAGCTCTTTTATTAATATCACACTTAATAAAAAATCCTAGTGATGGAATGCTT
ATCATATCAAAAATGATGTCACAATCACCTCTTGATGCATTGTCAGTTTTCACACAATTC
ATGACTTCACCATTTGACGCACTACAAATAATTTTTAAAGTAATGTCATCACCGAAAGAC
GTTTTAGCATTTATGACAGAGCTCACAAAATCACCACAAAATGCACTTGAGATTATGAAC
AAATTTATAACAACGCCATCGGAAAAAACAGTGACGGAATCATCACAAGAATTAAACAGT
AACTGTAACGAAACAATAAAATCAATGTTGGATGTTAATTCTAGTAATAGCAGTCCAAAT
CCTATTGTATCATCGTCATCATTTATTTCATCACAAACGACAACTAATTCACCAACAAGT
TTCTATCAAGATTCTGATTCGAACAACAATGACTATCAACAAATGACAACTACAATACTT
AGAGAAATTGCATACGATATATCTGTTGGTGGAAAACAATCTGTATCATCAAAAGAAAAT
TCAATTGATTCAATAATAAGTGAGGCAATAAAACTTGAATATAGTACTCCACAAATGGTA
GCACAAATGAAAAATCAAAGTCGTGAACTAAACGAAGTGGAAATTATGAAAATTCAGGAA
CTATTAGATGCAAATTGTGCCTTATATGCACCTATCGAGGAAGATCAATTTTCATTTTTT
GGCATGAGTGACGATCTATCAATTAAAGCTGATGGCACTCATTTCTTTGATCCAGTTCTG
ATGAAAGTAATTAATCTTACTGCTGTTGCAATTCGTCGTTTAATAAAAATGTCAAAGAAA
ATTTCTGGTTTTAAAAAGATGTGTCAAGTAGATCAAATTGCTTTGTTGAAGGGTGGCTGT
ACAGAAATGATGATTCTAAGGTCTGTAATGCAATACGATTCCGAACAATCTTTTTGGAAA
ATCCCATCAATGAGCACCACAAATTTAAAAACTGACATTCTGAAACTGTGTCCAAAAGGA
AACGTTTATGAGGAACATGAAAATTTTATTAAAACATTTGATTTAAAACTCCGTACTGAT
GAGAGAATTGTTCTTATATTATGCGCTATAACTCTTTTTAGTCCTCATCGTTCAAATGTA
ATTCATAAAGATGTGATAGCTTTGGAACAGAATTCGTATTATTTTCTTCTGCGTCGTTAT
CTTGAAAGCGTATATGAAGGTTGTGAGGCTCGCTCAATTTTTTTACAACTGCTAAGAAAA
ATTAATGAAGTGAGAAGATTAAATGAAGAAGTTATATCAGTATATTTGGATGTGGAGCCA
AGCAAAGTGGAGCCATTACTGAGAGAGATTTTTGATTTAAAAGCATAA
>g779.t1 Gene=g779 Length=655
MSRQSNEKICTICGDKSLGFNFNVISCESCKAFFRRNAISNKKFTCPFSNACEITVITRR
FCQKCRLEKCFKQGMKKEYIMSEEDKELKRIKIEQNRSKRKMKKEGTESSEESKPSKLTK
IKDEGWSPLSTSSVQSPDSKSEDSIDHTTTLDRLKISSDSSVAEIVNAITEIPKESSQII
QNVMKTQQEALSVMSRIIHEPNQALLLISHLIKNPSDGMLIISKMMSQSPLDALSVFTQF
MTSPFDALQIIFKVMSSPKDVLAFMTELTKSPQNALEIMNKFITTPSEKTVTESSQELNS
NCNETIKSMLDVNSSNSSPNPIVSSSSFISSQTTTNSPTSFYQDSDSNNNDYQQMTTTIL
REIAYDISVGGKQSVSSKENSIDSIISEAIKLEYSTPQMVAQMKNQSRELNEVEIMKIQE
LLDANCALYAPIEEDQFSFFGMSDDLSIKADGTHFFDPVLMKVINLTAVAIRRLIKMSKK
ISGFKKMCQVDQIALLKGGCTEMMILRSVMQYDSEQSFWKIPSMSTTNLKTDILKLCPKG
NVYEEHENFIKTFDLKLRTDERIVLILCAITLFSPHRSNVIHKDVIALEQNSYYFLLRRY
LESVYEGCEARSIFLQLLRKINEVRRLNEEVISVYLDVEPSKVEPLLREIFDLKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g779.t1 | CDD | cd06966 | NR_DBD_CAR | 8 | 100 | 2.81208E-55 |
| 13 | g779.t1 | CDD | cd06929 | NR_LBD_F1 | 463 | 630 | 6.75216E-44 |
| 12 | g779.t1 | Gene3D | G3DSA:3.30.50.10 | - | 7 | 107 | 1.3E-27 |
| 11 | g779.t1 | Gene3D | G3DSA:1.10.565.10 | Retinoid X Receptor | 407 | 654 | 1.2E-60 |
| 18 | g779.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 121 | - |
| 19 | g779.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 122 | - |
| 20 | g779.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 127 | 146 | - |
| 3 | g779.t1 | PANTHER | PTHR24082 | NUCLEAR HORMONE RECEPTOR | 3 | 653 | 8.9E-144 |
| 4 | g779.t1 | PANTHER | PTHR24082:SF283 | NUCLEAR HORMONE RECEPTOR HR96 | 3 | 653 | 8.9E-144 |
| 7 | g779.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 10 | 26 | 5.8E-12 |
| 8 | g779.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 26 | 41 | 5.8E-12 |
| 6 | g779.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 59 | 67 | 5.8E-12 |
| 5 | g779.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 67 | 75 | 5.8E-12 |
| 2 | g779.t1 | Pfam | PF00105 | Zinc finger, C4 type (two domains) | 9 | 77 | 1.6E-21 |
| 1 | g779.t1 | Pfam | PF00104 | Ligand-binding domain of nuclear hormone receptor | 462 | 632 | 5.9E-7 |
| 17 | g779.t1 | ProSitePatterns | PS00031 | Nuclear hormones receptors DNA-binding region signature. | 10 | 36 | - |
| 22 | g779.t1 | ProSiteProfiles | PS51030 | Nuclear hormone receptors DNA-binding domain profile. | 7 | 82 | 17.994 |
| 21 | g779.t1 | ProSiteProfiles | PS51843 | Nuclear receptor (NR) ligand-binding (LBD) domain profile. | 413 | 655 | 23.202 |
| 16 | g779.t1 | SMART | SM00399 | c4gold | 7 | 78 | 1.8E-31 |
| 15 | g779.t1 | SMART | SM00430 | holi | 465 | 628 | 2.9E-15 |
| 10 | g779.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 8 | 92 | 7.44E-27 |
| 9 | g779.t1 | SUPERFAMILY | SSF48508 | Nuclear receptor ligand-binding domain | 452 | 652 | 5.24E-43 |
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:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0043565 | sequence-specific DNA binding | MF |
| GO:0008270 | zinc ion binding | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14035 (nuclear receptor subfamily 1 group I)
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.
