Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Homeotic protein proboscipedia.

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 g4025 g4025.t2 isoform g4025.t2 29581582 29583748
chr_3 g4025 g4025.t2 exon g4025.t2.exon1 29581582 29582607
chr_3 g4025 g4025.t2 cds g4025.t2.CDS1 29581582 29582607
chr_3 g4025 g4025.t2 exon g4025.t2.exon2 29582895 29583235
chr_3 g4025 g4025.t2 cds g4025.t2.CDS2 29582895 29583235
chr_3 g4025 g4025.t2 exon g4025.t2.exon3 29583294 29583411
chr_3 g4025 g4025.t2 cds g4025.t2.CDS3 29583294 29583411
chr_3 g4025 g4025.t2 exon g4025.t2.exon4 29583569 29583748
chr_3 g4025 g4025.t2 cds g4025.t2.CDS4 29583569 29583748
chr_3 g4025 g4025.t2 TSS g4025.t2 NA NA
chr_3 g4025 g4025.t2 TTS g4025.t2 NA NA

Sequences

>g4025.t2 Gene=g4025 Length=1665
ATGTCGTTTCATTTATTTTTAGATGAATTCGTTGCAGAAAATGGACTGCCAAGGCGCCTA
CGGACAGCATATACAAATACACAGCTGTTGGAGCTTGAAAAGGAATTTCATTTTAATAAA
TATTTATGTCGACCAAGAAGGATCGAAATTGCAGCGAGTCTTGATCTTACTGAACGTCAG
GTCAAAGTATGGTTTCAGAACAGGAGAATGAAATTTAAGCGACAAACACAATCAAAAACA
GACGATGAAGATTCAAGTAAAGACGACTTTAAGGGTGATGATGACACACAATCATGCAAT
TCTAACTCGAAAAAGTCATGTCAAGGTTGCGAATTGCCATCCGATGATGTACCCGACTCC
ACATCGAATTCACGCGGTCAAAACAATAATACGCCTAGTGCAACCAACAATAATCAATCA
AATATTAATGAACGAACAAATGGTGCAATTTCAAGAACAACTCCCAATTCGACAATTGAT
TTGGGAACACCGCAAAATAATACACAGAGTTTGATCTCCAATGCAGACTCTTCAATTGCA
TCTACAGGTAGTCTCGATGACGATGAATTAGAGACGCCTGTGAAAATTAAAAAGAAAGAT
GAAACGACGAGTGGAGGTCGAAAGGTAAGGGGAAGAAATAAAAAAGAGCCAAAAGCATCA
TCACAACATAATATGTTTTCAAATAATGACGTCTATCGTAAGGAAAATGTGCAATCACCG
CACGTAATTGCGAAAGGCAATTTGAATTTTAATCGCGGCAACAACAACAATCAATATCAG
AATCAGGTTAAAATAAAGGGTCAACCAATAGTCGCAGCGATGCAGGAAGGTTACTTTCCT
GGATTTTATGGAAAACATCCACCTCCGAATATTCACCATCAACCAAACGATGTCATGTTT
GCAAAACACGAACTCGAATTTCATCAGAAAGGTTTGTCAACACCTCAACAACAACAGCCA
CAAAATCAGCAATTTCCACCATTTCATGGAGCTGCACAGAAGTATGAAATGCATGATTTT
GAACATCAACTTAAAAACGATAAAATGCCAATCGTCACAGGAGCTGGCATTCATGCTACA
CGTCCACCAATCGATTTTCCATCGCCACAAAATTCACAAATGTACTACAATGAAAATACA
GCTCAGAATTCACATAATCAATATTATCCGAATGAATTCGACATTGGAAATGACGCTGCA
AATGCTGTCAATGGAAATGTTAGTGGTGGGAGTAGCGGCGGTGGCTATTTTGATCAAAAA
TCTCAAGCACATTATTACGATATGAATTATCATCATCATAGTGGCGGCAATGATTATTCT
GACATGTATGCTGCCGGTCCAGGAAATGCAGCAGCAATTGTAAATGAAAATTGTGAAAAC
TTTGCATCATTCCAACAGTATTATGATCATCATCCACAACAACAGCAGCAACAGCAGCAA
AATATGCATGCACATCCACACCATTATCCGCCACATCATCATGTCGCACATCAACAAAAT
TTAACAAATCCAATTGCCACAGCTTATGTTCATCATCAACAAAATTTTGCATCAAATGCA
CAAATTCATGGCACAAATCTAACTGAAAATAGCAACAGTTCATCAGATTTTAATTTCTTG
AGTAATTTAAATGATTTTGCGCCTGAATATTATCAATTGAGTTAG

>g4025.t2 Gene=g4025 Length=554
MSFHLFLDEFVAENGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQ
VKVWFQNRRMKFKRQTQSKTDDEDSSKDDFKGDDDTQSCNSNSKKSCQGCELPSDDVPDS
TSNSRGQNNNTPSATNNNQSNINERTNGAISRTTPNSTIDLGTPQNNTQSLISNADSSIA
STGSLDDDELETPVKIKKKDETTSGGRKVRGRNKKEPKASSQHNMFSNNDVYRKENVQSP
HVIAKGNLNFNRGNNNNQYQNQVKIKGQPIVAAMQEGYFPGFYGKHPPPNIHHQPNDVMF
AKHELEFHQKGLSTPQQQQPQNQQFPPFHGAAQKYEMHDFEHQLKNDKMPIVTGAGIHAT
RPPIDFPSPQNSQMYYNENTAQNSHNQYYPNEFDIGNDAANAVNGNVSGGSSGGGYFDQK
SQAHYYDMNYHHHSGGNDYSDMYAAGPGNAAAIVNENCENFASFQQYYDHHPQQQQQQQQ
NMHAHPHHYPPHHHVAHQQNLTNPIATAYVHHQQNFASNAQIHGTNLTENSNSSSDFNFL
SNLNDFAPEYYQLS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4025.t2 CDD cd00086 homeodomain 18 75 6.17676E-25
8 g4025.t2 Gene3D G3DSA:1.10.10.60 - 11 79 2.2E-28
16 g4025.t2 MobiDBLite mobidb-lite consensus disorder prediction 72 143 -
12 g4025.t2 MobiDBLite mobidb-lite consensus disorder prediction 74 95 -
15 g4025.t2 MobiDBLite mobidb-lite consensus disorder prediction 96 143 -
13 g4025.t2 MobiDBLite mobidb-lite consensus disorder prediction 182 230 -
14 g4025.t2 MobiDBLite mobidb-lite consensus disorder prediction 188 219 -
2 g4025.t2 PANTHER PTHR45664 PROTEIN ZERKNUELLT 1-RELATED 11 497 7.8E-64
3 g4025.t2 PANTHER PTHR45664:SF2 HOMEOTIC PROTEIN PROBOSCIPEDIA 11 497 7.8E-64
6 g4025.t2 PRINTS PR00024 Homeobox signature 39 50 1.6E-7
4 g4025.t2 PRINTS PR00024 Homeobox signature 54 64 1.6E-7
5 g4025.t2 PRINTS PR00024 Homeobox signature 64 73 1.6E-7
1 g4025.t2 Pfam PF00046 Homeodomain 18 74 1.4E-21
11 g4025.t2 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 50 73 -
17 g4025.t2 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 15 75 21.135
10 g4025.t2 SMART SM00389 HOX_1 17 79 2.2E-28
7 g4025.t2 SUPERFAMILY SSF46689 Homeodomain-like 13 75 4.19E-25

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:0003677 DNA binding MF
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific MF
GO:0006355 regulation of transcription, DNA-templated BP

KEGG

Orthology

Pathway

This gene does not belong to any 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. There were no conditions that were differentially expressed