Gene loci information

Transcript annotation

  • This transcript has been annotated as Nuclear hormone receptor HR96.

Parent gene

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.t2 TTS g779.t2 5977227 5977227
chr_3 g779 g779.t2 isoform g779.t2 5978073 5979641
chr_3 g779 g779.t2 exon g779.t2.exon1 5978073 5979530
chr_3 g779 g779.t2 cds g779.t2.CDS1 5978073 5979530
chr_3 g779 g779.t2 exon g779.t2.exon2 5979609 5979641
chr_3 g779 g779.t2 cds g779.t2.CDS2 5979609 5979641
chr_3 g779 g779.t2 TSS g779.t2 5979793 5979793

Sequences

>g779.t2 Gene=g779 Length=1491
ATGAGCAGACAATCAAATGAAAAAATCTGCACGATTTGTGGAGACAAATCACTAGGGTTC
AATTTCAATGTGATAAGTTGTGAAAGCTGTAAGGCATTTTTTCGACGAAATGCAATTTCT
AATAAGAAATTTACATGCCCATTTTCTAATGCCTGTGAGATAACCGTGATAACACGACGA
TTTTGCCAAAAATGTCGATTAGAAAAGTGTTTCAAGCAAGGAATGAAAAAAGAATACATA
ATGTCAGAAGAGGATAAAGAGTTAAAGCGAATTAAAATTGAACAAAATCGCAGTAAAAGA
AAGATGAAAAAGGAGGGAACAGAAAGCAGTGAGGAGAGTAAACCTTCGAAATTGACAAAA
ATCAAAGATGAAGGTTGGTCACCATTATCGACATCATCTGTACAATCACCAGATAGTAAA
TCAGAAGATTCCATTGATCATACTACAACTCTCGATCGATTAAAAATAAGTTCCGATTCT
TCAGTGGCAGAAATTGTAAATGCTATTACAGAAATTCCAAAAGAATCTAGTCAAATAATT
CAAAATGTAATGAAAACACAACAAGAGGCATTGAGTGTCATGAGTAGAATCATTCATGAG
CCTAATCAAGCTCTTTTATTAATATCACACTTAATAAAAAATCCTAGTGATGGAATGCTT
ATCATATCAAAAATGATGTCACAATCACCTCTTGATGCATTGTCAGTTTTCACACAATTC
ATGACTTCACCATTTGACGCACTACAAATAATTTTTAAAGTAATGTCATCACCGAAAGAC
GTTTTAGCATTTATGACAGAGCTCACAAAATCACCACAAAATGCACTTGAGATTATGAAC
AAATTTATAACAACGCCATCGGAAAAAACAGTGACGGAATCATCACAAGAATTAAACAGT
AACTGTAACGAAACAATAAAATCAATGTTGGATGTTAATTCTAGTAATAGCAGTCCAAAT
CCTATTGTATCATCGTCATCATTTATTTCATCACAAACGACAACTAATTCACCAACAAGT
TTCTATCAAGATTCTGATTCGAACAACAATGACTATCAACAAATGACAACTACAATACTT
AGAGAAATTGCATACGATATATCTGTTGGTGGAAAACAATCTGTATCATCAAAAGAAAAT
TCAATTGATTCAATAATAAGTGAGGCAATAAAACTTGAATATAGTACTCCACAAATGGTA
GCACAAATGAAAAATCAAAGTCGTGAACTAAACGAAGTGGAAATTATGAAAATTCAGGAA
CTATTAGATGCAAATTGTGCCTTATATGCACCTATCGAGGAAGATCAATTTTCATTTTTT
GGCATGAGTGACGATCTATCAATTAAAGCTGATGGCACTCATTTCTTTGATCCAGTTCTG
ATGAAAGTAATTAATCTTACTGCTGTTGCAATTCGTCGTTTAATAAAAATGTCAAAGAAA
ATTTCTGGTTTTAAAAAGATGTGTCAAGTAGATCAAATTGCTTTGTTGAAG

>g779.t2 Gene=g779 Length=497
MSRQSNEKICTICGDKSLGFNFNVISCESCKAFFRRNAISNKKFTCPFSNACEITVITRR
FCQKCRLEKCFKQGMKKEYIMSEEDKELKRIKIEQNRSKRKMKKEGTESSEESKPSKLTK
IKDEGWSPLSTSSVQSPDSKSEDSIDHTTTLDRLKISSDSSVAEIVNAITEIPKESSQII
QNVMKTQQEALSVMSRIIHEPNQALLLISHLIKNPSDGMLIISKMMSQSPLDALSVFTQF
MTSPFDALQIIFKVMSSPKDVLAFMTELTKSPQNALEIMNKFITTPSEKTVTESSQELNS
NCNETIKSMLDVNSSNSSPNPIVSSSSFISSQTTTNSPTSFYQDSDSNNNDYQQMTTTIL
REIAYDISVGGKQSVSSKENSIDSIISEAIKLEYSTPQMVAQMKNQSRELNEVEIMKIQE
LLDANCALYAPIEEDQFSFFGMSDDLSIKADGTHFFDPVLMKVINLTAVAIRRLIKMSKK
ISGFKKMCQVDQIALLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g779.t2 CDD cd06966 NR_DBD_CAR 8 100 5.07279E-56
11 g779.t2 Gene3D G3DSA:3.30.50.10 - 7 107 8.6E-28
10 g779.t2 Gene3D G3DSA:1.10.565.10 Retinoid X Receptor 407 497 1.3E-12
15 g779.t2 MobiDBLite mobidb-lite consensus disorder prediction 91 121 -
16 g779.t2 MobiDBLite mobidb-lite consensus disorder prediction 91 122 -
17 g779.t2 MobiDBLite mobidb-lite consensus disorder prediction 127 146 -
2 g779.t2 PANTHER PTHR24082 NUCLEAR HORMONE RECEPTOR 3 497 3.2E-75
3 g779.t2 PANTHER PTHR24082:SF283 NUCLEAR HORMONE RECEPTOR HR96 3 497 3.2E-75
6 g779.t2 PRINTS PR00047 C4-type steroid receptor zinc finger signature 10 26 2.2E-12
7 g779.t2 PRINTS PR00047 C4-type steroid receptor zinc finger signature 26 41 2.2E-12
5 g779.t2 PRINTS PR00047 C4-type steroid receptor zinc finger signature 59 67 2.2E-12
4 g779.t2 PRINTS PR00047 C4-type steroid receptor zinc finger signature 67 75 2.2E-12
1 g779.t2 Pfam PF00105 Zinc finger, C4 type (two domains) 9 77 1.1E-21
14 g779.t2 ProSitePatterns PS00031 Nuclear hormones receptors DNA-binding region signature. 10 36 -
18 g779.t2 ProSiteProfiles PS51030 Nuclear hormone receptors DNA-binding domain profile. 7 82 17.994
13 g779.t2 SMART SM00399 c4gold 7 78 1.8E-31
9 g779.t2 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain) 8 92 4.89E-27
8 g779.t2 SUPERFAMILY SSF48508 Nuclear receptor ligand-binding domain 451 497 1.27E-8

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values