Gene loci information

Transcript annotation

  • This transcript has been annotated as Pleiotropic regulator 1.

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 g2438 g2438.t1 TTS g2438.t1 18002659 18002659
chr_3 g2438 g2438.t1 isoform g2438.t1 18002692 18004111
chr_3 g2438 g2438.t1 exon g2438.t1.exon1 18002692 18003940
chr_3 g2438 g2438.t1 cds g2438.t1.CDS1 18002692 18003940
chr_3 g2438 g2438.t1 exon g2438.t1.exon2 18003996 18004111
chr_3 g2438 g2438.t1 cds g2438.t1.CDS2 18003996 18004111
chr_3 g2438 g2438.t1 TSS g2438.t1 18004200 18004200

Sequences

>g2438.t1 Gene=g2438 Length=1365
ATGGAAGAAGTTCAAAGGCATTCAGTACATACTTTAGTATTTCGTTCATTAAAAAGAAGT
CACGATTTATTCGTCAGCAATCAACCGATTGTAAATTTAGAGGCCGATGAAAAATCCGAA
AAAATGAGATTTAATATAAAAGCAAGAGATTCGTATGCTCCAATTTTTCATCGTGTAGCA
GTTTCAGAGCAAGAACAGAAGAAGGCCGAATATTTTAATAAATCGGACGAACCTATAACA
AAAGGCGATGAAATGGCTCTTGTTCCTTCTACACAATCTCAAAATGATCAAACTTCATCA
GCATTATTGCCATTACCTACAACAACACATAATACAAATCAACAACAATTGATTCCTAAA
AAGCCTTCATCAATACCAAAGCCAAAATGGCATGCACCATGGAAATTGTATCGAGTAATT
AGCGGTCATTTGGGTTGGGTTAGATGTGCAGCTGTTGAACCTGGAAATGAATGGTTTGCA
ACTGGTGCAGCAGATCGAGTGATTAAAGTTTGGGATTTGGCAAGTGGAAAATTAAAATTA
TCGCTAACAGGTCATGTAAGCACAGTAAGAGGACTTGCTGTAAGTGCACGTCATCCATAT
CTTTTTTCATGTGGTGAAGATCGTCAAGTAAAATGCTGGGATTTGGAATATAATAAAGTA
ATAAGGCATTATCACGGTCACTTGTCTGCCGTCTATACAATGGCTCTTCATCCAACACTC
GATATTCTTGTAACAGCTGGTCGTGACTCAACTGCGCGCGTTTGGGATATGAGAACAAAA
GCAAATATTCATACACTCACAGGACATACAAATACAGTTGCAAGTGTTGTCACACAAGCT
GCCAATCCTCAAATTATAACGGGAAGTCATGATTCGACAGTAAGATTATGGGATTTGGCT
GCAGGTAAAAGTCTTTGTACACTGACAAATCATAAAAAGAGCGTTCGTAGTGTTGTTCTT
CATCCAACTCTCTATATGTTTGCATCTGCAAGTCCTGATAATATCAAACAATGGCGTTGT
CCCGAAGGAAATTTCGTACAAAATTTATCGGGGCATAATACAATTGTTAATTGCATGGCT
GTCAATCCTGAAGGAGTTTTAGTTTCTGGTGGTGACAATGGAAGCATGAATTTCTGGGAT
TGGAGAACAGGATATAATTTCCAGCGTTTTCAAGCTGCAGTTCAACCTGGTTCAATGGAT
TCTGAAGCTGGAATTTTCTCAATGACTTTTGATCAATCTGGATCAAGATTAATAACTACA
GAAGCTGACAAGACTATTAAAATATACAAGGAAGATGATGAAGCGAGTGAAGAAACTCAT
CCAGTAAATTGGAAACCAGATATCATTAAGCGACGTAAATATTAA

>g2438.t1 Gene=g2438 Length=454
MEEVQRHSVHTLVFRSLKRSHDLFVSNQPIVNLEADEKSEKMRFNIKARDSYAPIFHRVA
VSEQEQKKAEYFNKSDEPITKGDEMALVPSTQSQNDQTSSALLPLPTTTHNTNQQQLIPK
KPSSIPKPKWHAPWKLYRVISGHLGWVRCAAVEPGNEWFATGAADRVIKVWDLASGKLKL
SLTGHVSTVRGLAVSARHPYLFSCGEDRQVKCWDLEYNKVIRHYHGHLSAVYTMALHPTL
DILVTAGRDSTARVWDMRTKANIHTLTGHTNTVASVVTQAANPQIITGSHDSTVRLWDLA
AGKSLCTLTNHKKSVRSVVLHPTLYMFASASPDNIKQWRCPEGNFVQNLSGHNTIVNCMA
VNPEGVLVSGGDNGSMNFWDWRTGYNFQRFQAAVQPGSMDSEAGIFSMTFDQSGSRLITT
EADKTIKIYKEDDEASEETHPVNWKPDIIKRRKY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g2438.t1 CDD cd00200 WD40 136 430 4.06539E-91
12 g2438.t1 Gene3D G3DSA:2.130.10.10 - 137 432 5.7E-117
6 g2438.t1 PANTHER PTHR19923:SF0 PLEIOTROPIC REGULATOR 1 2 449 2.4E-189
7 g2438.t1 PANTHER PTHR19923 WD40 REPEAT PROTEINPRL1/PRL2-RELATED 2 449 2.4E-189
9 g2438.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 159 173 1.2E-7
10 g2438.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 243 257 1.2E-7
8 g2438.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 285 299 1.2E-7
1 g2438.t1 Pfam PF00400 WD domain, G-beta repeat 135 172 8.1E-7
3 g2438.t1 Pfam PF00400 WD domain, G-beta repeat 177 214 1.0E-5
4 g2438.t1 Pfam PF00400 WD domain, G-beta repeat 219 256 2.9E-5
2 g2438.t1 Pfam PF00400 WD domain, G-beta repeat 262 298 8.0E-6
5 g2438.t1 Pfam PF00400 WD domain, G-beta repeat 344 380 3.7E-5
15 g2438.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 243 257 -
14 g2438.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 285 299 -
23 g2438.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 140 439 59.532
28 g2438.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 140 181 13.65
25 g2438.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 182 223 12.313
24 g2438.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 224 265 15.388
27 g2438.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 266 307 15.187
26 g2438.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 349 389 11.912
18 g2438.t1 SMART SM00320 WD40_4 133 172 6.3E-8
21 g2438.t1 SMART SM00320 WD40_4 175 214 4.4E-7
17 g2438.t1 SMART SM00320 WD40_4 217 256 6.4E-7
20 g2438.t1 SMART SM00320 WD40_4 259 298 1.4E-6
16 g2438.t1 SMART SM00320 WD40_4 301 339 2.8E-4
19 g2438.t1 SMART SM00320 WD40_4 342 380 1.9E-6
22 g2438.t1 SMART SM00320 WD40_4 392 430 1.6
11 g2438.t1 SUPERFAMILY SSF50978 WD40 repeat-like 130 430 7.99E-78

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:0005515 protein binding MF

KEGG

Orthology

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.

Raw TPM values