General information for g5831.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable nuclear hormone receptor HR38.
Parent gene
- The parent gene g5831 is located on chr_2: 12158830..12191471 (+ 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 | g5831 | g5831.t1 | TSS | g5831.t1 | 12158561 | 12158561 |
| chr_2 | g5831 | g5831.t1 | isoform | g5831.t1 | 12158830 | 12191471 |
| chr_2 | g5831 | g5831.t1 | exon | g5831.t1.exon1 | 12158830 | 12159001 |
| chr_2 | g5831 | g5831.t1 | cds | g5831.t1.CDS1 | 12158830 | 12159001 |
| chr_2 | g5831 | g5831.t1 | exon | g5831.t1.exon2 | 12187808 | 12187932 |
| chr_2 | g5831 | g5831.t1 | cds | g5831.t1.CDS2 | 12187808 | 12187932 |
| chr_2 | g5831 | g5831.t1 | exon | g5831.t1.exon3 | 12188877 | 12189641 |
| chr_2 | g5831 | g5831.t1 | cds | g5831.t1.CDS3 | 12188877 | 12189641 |
| chr_2 | g5831 | g5831.t1 | exon | g5831.t1.exon4 | 12189704 | 12190790 |
| chr_2 | g5831 | g5831.t1 | cds | g5831.t1.CDS4 | 12189704 | 12190790 |
| chr_2 | g5831 | g5831.t1 | exon | g5831.t1.exon5 | 12191215 | 12191471 |
| chr_2 | g5831 | g5831.t1 | cds | g5831.t1.CDS5 | 12191215 | 12191471 |
| chr_2 | g5831 | g5831.t1 | TTS | g5831.t1 | NA | NA |
Sequences
>g5831.t1 Gene=g5831 Length=2406
ATGAGAACAGAACTTGCACCATTGATTGTTGTAAAGCAGGAATTTCCAGACTTTCGCATC
AATGGCAGTGAAAATGGTGAAGAGAACAATAATAACTTTATGATTATTAAAAGTGAAAAT
GATTGCAATAATAATCAGCCTGAGGATTTAAATTCGCTTTCAGTGAAAAAGAGTGCATCA
ATATCTGATCGATCTCAAGCAGAAGGAAATCTCAGCGAAGAGCGAAGCATCACCGTTCGT
CGAAGTCTCACGGATAGCCTCGCTGTGTCAAGCATGTTGTTATTGCAACCACAGCAAAGT
TCTTTCAGTTCTATCTCACCATCGCTTGATTTTCTTTTATTACAACAGCAGCAACAGCAA
GAAGAATTGCTAAATCAGCAGCAGCAATCAATTCACAACCTCGAATCGTCATTTTCTGAC
ATTTTATTTTCACAAAATCAACAAGATCGCGCATTCATTGAACATCAGACGCAGCATTCA
AATTCATCAAGTGATACACTTGTTGGCATTGAAGAAGAAACGTCGCAAGATTTATTGACG
CCTACAATAACACAATTTAAAGAGGAGCCACCATTTCTGACGCATCCACATACACCGACA
AATCCACGTAGTGTCGAACAAGAGCAAGATTTGATTTTTGAAACATCGTCAACAGAAGAA
CTTGGTTTATTGAGTTTAAGATCAAGCAGTGATCCAACACTTTCAAATACTTCAAATCAA
GCTGCTTCAGTGAGTGCACAACAACAAGCACAGCAGCGACCACAAACATCAACAGCAGCA
GAATTGCTTGATGTAAATCCAATTTTACCGAGCTTTCAAGAAACTTATCCAATAAAATAC
AATCAACTTGCCGACTTTGGCCTAAAAATGGACGAAGATTGCTTTAATGTTGCCGCTGCT
GCTGCAGCTGCTGCAAGTTCTCATCCAGCTAACGTTCCAACATATCAACAAGGTCATCAT
ACAAATGCGCCTTATGGCTTTCAAGGTCCACATTCTGAATATTTGCAGAATGTTGGCAGT
AGCTTTTATCAGCACCATCATCATTATGAACCACATTCATTGTATGGCACAACATCATCA
CATGAAACATATTCTCTGCCAACATTCCCAACCGTGACAGATCTCAATGTGTCAGCAGCA
GTCAGTCGACGTGCTTCTTTGCCTCTTCAACGATCCGAATCGACATCGAGCAGCGAAAGC
CCAAAACCAGCGGCTAAAATATCTGGCATCTACAGCAAATACTCGACTGCAATGCAGAGT
ACTTCCAGTTCAGCATCAAGTTCGCCCTCGTGCATTAACAACAACAATCCAAGTGTTGCA
AATGCGAATGTTGATGTTTCAAGTCTTGCTACAATGGGCGCAACTGCTAAAATTCAACAT
CAAAATCCATCACAGTTATGTGCTGTTTGTGGTGATACAGCCGCTTGCCAGCATTATGGT
GTACGCACATGTGAAGGTTGCAAAGGCTTTTTTAAACGCACAGTGCAAAAGGGTGCAAAA
TACGTTTGCTTGGCTGACAAGGCTTGTCCAGTCGATAAACGACGACGAAATCGTTGCCAG
TTCTGCCGATTCCAAAAATGCCTCGCCGTTGGCATGGTCAAAGAGGTTGTACGAACTGAC
TCGCTAAAGGGAAGACGTGGTCGACTGCCATCGAAACCAAAATCACCGCAAGAGTCGCCT
CCATCACCGCCTGTCTCGTTGATTACGGCTTTAGTGCGTGCACATGTTGACACAAGTCCC
GATCTCTCGACACTCGATTACAATCAATATCGTGAGCCATCGCTGATCGAACCAACAATT
TCTGAAGCAGAAAAAATTCAACAGTTCTATAATCTCCTGACAACTTCCGTCGATGTAATC
AAACATTTTGCTGAAAAACTGCCTGGCTTCAATGAATTATGTCGCGAAGATCAGGATCTA
CTATTTCAATCTGCTTCCCTTGAGCTATTTGTGCTACGACTCTCATATCGTGCACACATC
GATGATACAAAGATGGTATTTTGTAATGGAACCGTTTTACATAAGCAACAGTGTCAGCGT
TCATTTGGTGATTGGTTGAATGCCATTCTCGAGTTCAGCAATAGCCTGCACGCAATGGAA
ATTGATATTTCAGCCTTTGCGTGCCTTTGCGCTTTAACACTCGTCACAGAGCGCCACGGC
TTGAAAGAACCGAAGAAGGTTGAACAATTACAATTGAAAGTGATTAATAGTCTCCGCGAT
CATGTCACATATAACTCGGAGGCTCAACGAAAGCCGCATTACTTCAGTCGATTGCTGGGT
AAATTACCTGAATTACGTTCGCTAAGTGTTCAAGGCTTGCAGCGAATCTTTTATTTGAAA
CTGGAAGACTTGGTTCCTGCTCCGCCACTTATTGAGAACATGTTTGTTGCCAGCTTGCCT
TTCTAA
>g5831.t1 Gene=g5831 Length=801
MRTELAPLIVVKQEFPDFRINGSENGEENNNNFMIIKSENDCNNNQPEDLNSLSVKKSAS
ISDRSQAEGNLSEERSITVRRSLTDSLAVSSMLLLQPQQSSFSSISPSLDFLLLQQQQQQ
EELLNQQQQSIHNLESSFSDILFSQNQQDRAFIEHQTQHSNSSSDTLVGIEEETSQDLLT
PTITQFKEEPPFLTHPHTPTNPRSVEQEQDLIFETSSTEELGLLSLRSSSDPTLSNTSNQ
AASVSAQQQAQQRPQTSTAAELLDVNPILPSFQETYPIKYNQLADFGLKMDEDCFNVAAA
AAAAASSHPANVPTYQQGHHTNAPYGFQGPHSEYLQNVGSSFYQHHHHYEPHSLYGTTSS
HETYSLPTFPTVTDLNVSAAVSRRASLPLQRSESTSSSESPKPAAKISGIYSKYSTAMQS
TSSSASSSPSCINNNNPSVANANVDVSSLATMGATAKIQHQNPSQLCAVCGDTAACQHYG
VRTCEGCKGFFKRTVQKGAKYVCLADKACPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTD
SLKGRRGRLPSKPKSPQESPPSPPVSLITALVRAHVDTSPDLSTLDYNQYREPSLIEPTI
SEAEKIQQFYNLLTTSVDVIKHFAEKLPGFNELCREDQDLLFQSASLELFVLRLSYRAHI
DDTKMVFCNGTVLHKQQCQRSFGDWLNAILEFSNSLHAMEIDISAFACLCALTLVTERHG
LKEPKKVEQLQLKVINSLRDHVTYNSEAQRKPHYFSRLLGKLPELRSLSVQGLQRIFYLK
LEDLVPAPPLIENMFVASLPF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g5831.t1 | CDD | cd06969 | NR_DBD_NGFI-B | 465 | 539 | 1.06875E-53 |
| 19 | g5831.t1 | CDD | cd07072 | NR_LBD_DHR38_like | 567 | 801 | 9.10397E-166 |
| 18 | g5831.t1 | Coils | Coil | Coil | 109 | 137 | - |
| 17 | g5831.t1 | Gene3D | G3DSA:3.30.50.10 | - | 457 | 557 | 9.9E-32 |
| 16 | g5831.t1 | Gene3D | G3DSA:1.10.565.10 | Retinoid X Receptor | 558 | 801 | 4.1E-100 |
| 27 | g5831.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 229 | 257 | - |
| 24 | g5831.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 385 | 403 | - |
| 25 | g5831.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 385 | 404 | - |
| 26 | g5831.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 564 | - |
| 3 | g5831.t1 | PANTHER | PTHR24085 | NUCLEAR HORMONE RECEPTOR | 94 | 801 | 1.6E-224 |
| 4 | g5831.t1 | PANTHER | PTHR24085:SF4 | NUCLEAR HORMONE RECEPTOR HR38-RELATED | 94 | 801 | 1.6E-224 |
| 8 | g5831.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 467 | 483 | 1.3E-16 |
| 6 | g5831.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 483 | 498 | 1.3E-16 |
| 5 | g5831.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 516 | 524 | 1.3E-16 |
| 7 | g5831.t1 | PRINTS | PR00047 | C4-type steroid receptor zinc finger signature | 524 | 532 | 1.3E-16 |
| 11 | g5831.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 528 | 538 | 4.3E-20 |
| 13 | g5831.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 612 | 633 | 4.3E-20 |
| 10 | g5831.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 633 | 649 | 4.3E-20 |
| 9 | g5831.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 699 | 714 | 4.3E-20 |
| 12 | g5831.t1 | PRINTS | PR00398 | Steroid hormone receptor signature | 757 | 774 | 4.3E-20 |
| 2 | g5831.t1 | Pfam | PF00105 | Zinc finger, C4 type (two domains) | 465 | 534 | 1.9E-29 |
| 1 | g5831.t1 | Pfam | PF00104 | Ligand-binding domain of nuclear hormone receptor | 605 | 781 | 6.2E-26 |
| 23 | g5831.t1 | ProSitePatterns | PS00031 | Nuclear hormones receptors DNA-binding region signature. | 467 | 493 | - |
| 29 | g5831.t1 | ProSiteProfiles | PS51030 | Nuclear hormone receptors DNA-binding domain profile. | 464 | 539 | 19.57 |
| 28 | g5831.t1 | ProSiteProfiles | PS51843 | Nuclear receptor (NR) ligand-binding (LBD) domain profile. | 563 | 798 | 54.984 |
| 22 | g5831.t1 | SMART | SM00399 | c4gold | 464 | 535 | 3.2E-37 |
| 21 | g5831.t1 | SMART | SM00430 | holi | 611 | 769 | 1.0E-30 |
| 15 | g5831.t1 | SUPERFAMILY | SSF57716 | Glucocorticoid receptor-like (DNA-binding domain) | 464 | 543 | 2.75E-27 |
| 14 | g5831.t1 | SUPERFAMILY | SSF48508 | Nuclear receptor ligand-binding domain | 538 | 798 | 5.77E-67 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5831/g5831.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5831.t1.fa.iupred3.txt does not exist
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 K08558 (nuclear receptor subfamily 4 group A member 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.
