Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Prolactin regulatory element-binding protein.

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_1 g9619 g9619.t1 TTS g9619.t1 4305152 4305152
chr_1 g9619 g9619.t1 isoform g9619.t1 4305218 4306654
chr_1 g9619 g9619.t1 exon g9619.t1.exon1 4305218 4305303
chr_1 g9619 g9619.t1 cds g9619.t1.CDS1 4305218 4305303
chr_1 g9619 g9619.t1 exon g9619.t1.exon2 4305367 4306502
chr_1 g9619 g9619.t1 cds g9619.t1.CDS2 4305367 4306502
chr_1 g9619 g9619.t1 exon g9619.t1.exon3 4306569 4306654
chr_1 g9619 g9619.t1 cds g9619.t1.CDS3 4306569 4306654
chr_1 g9619 g9619.t1 TSS g9619.t1 4306739 4306739

Sequences

>g9619.t1 Gene=g9619 Length=1308
ATGGGGTCGAAAAAGAACATGATAACCGATTGCCTTTTAGCCAAAGTAAATTTTCCACTT
TATGCTGCTGAAATGCTAACAAGCAGACATTTGCTTGTCGCTGGTGGCGGTGGCTCAGCG
AAAACTGGAGTAGCAAATGGTTTTGAAATATATGAATTGTATCACAATGGAAAGTATTTT
GTGGCAGAAGAAATACAAAGACACGAAACAGGGTCAAGAGCCGTAATGAATATGTCATTA
AAACACATCGATCGAAGAGCACTGCTCGTTGCTGGTCAAGAAGGCCATAGTCAAATGTTT
GTTATCAGTTCAAAAGTAGGTCAATTGCCTACAAAAGAAACTCAAATTTCGAGTCGAAGG
GAATCATCATCAACGGAAGTTAGACAAAGAAGAAGAACAGAATCTACGAGTCAAGATACT
CCTAAATCTCAAATATCGACAACAACTGACTCCTCAGGAAATCAAATGAAACGAATTTAC
TTCGATATTAAAGCTGCCGATTCAGTACAAACAGATTTTTCTACTGAACCTTATCAAAGA
GTCGTGAGAATTTGTTTAAATGGAAAATTCATGGCAACAGCAGGAATTGATGGCCACGTT
CGTATATGGCATTTTCCACGAATGACACCATTTCATGATATAAAAGCTCATGAGAAAGAG
TTGGATGACTTGGATTTTAGTCCAGATGGCAAATACTTAATATCAATTGCAAAAGATGGT
ATTGCATCAGTTTGGTCAGTGAACAATGGAAAAGAGGCTTTGAAATTGAAATGGACACCA
CCAGAGAATGTTAAATATTTATATAAAAGATGTCGATATTCAACAATTGAAGGAGAAACA
GACAAATATAGACTCTTTACAATATCAAATCCACTACATAAAGCTGGAAAACAAAGAGGA
TTTTTGCAACAATGGAATATTGAGACTGGTCGACTCAATAATATAGTTAGCATAGATGAA
AGCCTTTCAGCATTAGCCGTTCGTGATGATGGTCGTTTTGTATCAATTGGAACAATGTTT
ACTGGTTCAGTTATGATTTATATTGCATTTAGTTTACAACAAGTGCTTTATGTGCCGAAT
GCTCATTCAATGTTTGTCACTGGTCTTGAATTTATTCCAGTTCTAAATAAAGATGCACCG
CCAATTTCAAGTGACGCTGAAGCTTCTGTTATATCATACTCTGTTGACAATCGTATCTGC
ATTCATAGTTTGCAATATAGACATACGTTGCCAGCATGGGCTGCAATATTTTTAATAATT
GTTATTCTTTTCCTCACATTTTTAATGTGTTCTTACTTTGGTATATAA

>g9619.t1 Gene=g9619 Length=435
MGSKKNMITDCLLAKVNFPLYAAEMLTSRHLLVAGGGGSAKTGVANGFEIYELYHNGKYF
VAEEIQRHETGSRAVMNMSLKHIDRRALLVAGQEGHSQMFVISSKVGQLPTKETQISSRR
ESSSTEVRQRRRTESTSQDTPKSQISTTTDSSGNQMKRIYFDIKAADSVQTDFSTEPYQR
VVRICLNGKFMATAGIDGHVRIWHFPRMTPFHDIKAHEKELDDLDFSPDGKYLISIAKDG
IASVWSVNNGKEALKLKWTPPENVKYLYKRCRYSTIEGETDKYRLFTISNPLHKAGKQRG
FLQQWNIETGRLNNIVSIDESLSALAVRDDGRFVSIGTMFTGSVMIYIAFSLQQVLYVPN
AHSMFVTGLEFIPVLNKDAPPISSDAEASVISYSVDNRICIHSLQYRHTLPAWAAIFLII
VILFLTFLMCSYFGI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g9619.t1 MobiDBLite mobidb-lite consensus disorder prediction 111 152 -
17 g9619.t1 MobiDBLite mobidb-lite consensus disorder prediction 123 137 -
18 g9619.t1 MobiDBLite mobidb-lite consensus disorder prediction 138 152 -
3 g9619.t1 PANTHER PTHR23284 PROLACTIN REGULATORY ELEMENT BINDING PROTEIN 13 432 8.9E-89
4 g9619.t1 PANTHER PTHR23284:SF0 PROLACTIN REGULATORY ELEMENT-BINDING PROTEIN 13 432 8.9E-89
2 g9619.t1 Pfam PF00400 WD domain, G-beta repeat 185 203 0.078
1 g9619.t1 Pfam PF00400 WD domain, G-beta repeat 210 246 0.024
6 g9619.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 332 -
9 g9619.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 333 350 -
8 g9619.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 351 411 -
10 g9619.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 412 434 -
7 g9619.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 435 435 -
19 g9619.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 187 255 16.296
20 g9619.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 214 255 13.449
14 g9619.t1 SMART SM00320 WD40_4 166 204 2.5
15 g9619.t1 SMART SM00320 WD40_4 207 246 8.3E-5
13 g9619.t1 SMART SM00320 WD40_4 352 403 78.0
5 g9619.t1 SUPERFAMILY SSF50978 WD40 repeat-like 180 404 7.33E-23
12 g9619.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -
11 g9619.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 412 434 -

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