Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein gooseberry.

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 g3880 g3880.t1 TSS g3880.t1 28591249 28591249
chr_3 g3880 g3880.t1 isoform g3880.t1 28591476 28598851
chr_3 g3880 g3880.t1 exon g3880.t1.exon1 28591476 28591530
chr_3 g3880 g3880.t1 cds g3880.t1.CDS1 28591476 28591530
chr_3 g3880 g3880.t1 exon g3880.t1.exon2 28597190 28598450
chr_3 g3880 g3880.t1 cds g3880.t1.CDS2 28597190 28598450
chr_3 g3880 g3880.t1 exon g3880.t1.exon3 28598728 28598851
chr_3 g3880 g3880.t1 cds g3880.t1.CDS3 28598728 28598851
chr_3 g3880 g3880.t1 TTS g3880.t1 28599101 28599101

Sequences

>g3880.t1 Gene=g3880 Length=1440
ATGACGATGAGATCACTAGAACCAACACCATATTTTGCTGGATATCCATTTCAAGGTCAA
GGACGAGTGAACCAACTTGGTGGTGTTTTTATTAATGGAAGACCTTTGCCAAATCACATT
CGTTTGAAGATTGTTGAACTAGCTGCTGCTGGCGTACGACCCTGTGTAATTTCACGTCAG
CTACGCGTTTCGCATGGCTGTGTATCGAAAATTCTCAATCGCTATCAAGAGACTGGATCA
ATTCGACCCGGTGTAATTGGTGGCAGTAAACCGCGTGTCGCCACACCTGAAATTGAGAAT
CGTATAGAAGAAATGAAGAAAGAAAATCCGGGAATGTTTTCATGGGAAATTCGTGAGCAA
TTGATCAAAGAAGGTGTTTGTGATAAGCAATCAGCACCGTCAGTAAGCAGTATTAGTCGA
TTGTTAAGACAAAAGAATGTTGGCGATGGTGAAACTGAAATACCAAACAATTATTCAATC
AACGGAATTCTCGGACAATCGGACGAAAGTGATACAGAGTCAGAACCAGGTATTCAATTA
AAACGCAAACAACGTCGTTCAAGAACAACTTTCAATGGTGAACAATTAGAAGCACTCGAG
AGAGCTTTTGCAAGAACTCAATATCCAGATGTTTATACACGAGAAGATTTAGCTCATCAT
ACTAGCCTTACAGAGGCACGAGTACAAGTTTGGTTTTCAAATCGTCGTGCAAGACTTCGC
AAGCAACTCAATTCTCAACAAGTGCCGACATTTAACTCAAACTTGTCATCGTTCAGTTCA
CAATATGAAGCGCCTTTACAAATGCCAACAACACAGACATCATTTGCATCGAGTATGCAG
TCATGGACACAGCCGTACACAACCACACAACAATCATCATCGCAATCCTCGTCGTCTGCT
TTCAATCACCTTGCAGCAGCAGCAGCAGTTGCTCCAATCATCACTAGCTCAGCAGCTCTC
AGTCCTGCTTCATTAACTTCAAGTCCTGTGCACTCATCTGCATTGACCCAAACAACCTCA
GCATCATCAATCTCAAATAATAATAATAATAATAATATGAGCATGAGTTACAGCAATTAT
TCTTCATCTATGGCAGAACAACAGCACAGCAATTCGACGCCACCAATAGCAACACAAAAT
CACTTGAGTTCATCACCACCTACTCCACCGTCTGTAAGTGCAACTTCTTATCCATTTCAT
TCCTATGGCAGTGCAGTTTCATCCTTCGACCAGACTTCACAATGGCGTGCAGCAAGCATG
TCCATGCAAAACAAACCAACCATGCCAAATACTGGCTTCGAATGGGATGCTTATAGTTCC
TTTTTTGCAAGCAATATGAACCATTACCAACCAACAACAACCATGAGCGGACATTCGCTT
TCACCATCAAATGGAGATGTAAAGACTTATCATGGATTAGAAATTAATCGTGTTCACTAG

>g3880.t1 Gene=g3880 Length=479
MTMRSLEPTPYFAGYPFQGQGRVNQLGGVFINGRPLPNHIRLKIVELAAAGVRPCVISRQ
LRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPEIENRIEEMKKENPGMFSWEIREQ
LIKEGVCDKQSAPSVSSISRLLRQKNVGDGETEIPNNYSINGILGQSDESDTESEPGIQL
KRKQRRSRTTFNGEQLEALERAFARTQYPDVYTREDLAHHTSLTEARVQVWFSNRRARLR
KQLNSQQVPTFNSNLSSFSSQYEAPLQMPTTQTSFASSMQSWTQPYTTTQQSSSQSSSSA
FNHLAAAAAVAPIITSSAALSPASLTSSPVHSSALTQTTSASSISNNNNNNNMSMSYSNY
SSSMAEQQHSNSTPPIATQNHLSSSPPTPPSVSATSYPFHSYGSAVSSFDQTSQWRAASM
SMQNKPTMPNTGFEWDAYSSFFASNMNHYQPTTTMSGHSLSPSNGDVKTYHGLEINRVH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g3880.t1 CDD cd00131 PAX 19 145 9.39228E-84
15 g3880.t1 CDD cd00086 homeodomain 185 242 1.13723E-21
13 g3880.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 19 87 1.1E-37
12 g3880.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 88 146 1.0E-31
11 g3880.t1 Gene3D G3DSA:1.10.10.60 - 168 245 5.7E-28
21 g3880.t1 MobiDBLite mobidb-lite consensus disorder prediction 166 189 -
20 g3880.t1 MobiDBLite mobidb-lite consensus disorder prediction 174 189 -
22 g3880.t1 MobiDBLite mobidb-lite consensus disorder prediction 360 394 -
3 g3880.t1 PANTHER PTHR45636 PAIRED BOX PROTEIN PAX-6-RELATED-RELATED 1 372 2.5E-168
4 g3880.t1 PANTHER PTHR45636:SF3 PROTEIN GOOSEBERRY-RELATED 1 372 2.5E-168
8 g3880.t1 PRINTS PR00027 Paired box signature 23 38 1.9E-39
7 g3880.t1 PRINTS PR00027 Paired box signature 41 59 1.9E-39
6 g3880.t1 PRINTS PR00027 Paired box signature 61 78 1.9E-39
5 g3880.t1 PRINTS PR00027 Paired box signature 79 96 1.9E-39
2 g3880.t1 Pfam PF00292 ‘Paired box’ domain 19 143 1.9E-71
1 g3880.t1 Pfam PF00046 Homeodomain 185 241 1.9E-21
18 g3880.t1 ProSitePatterns PS00034 Paired DNA-binding domain signature. 53 69 -
19 g3880.t1 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 217 240 -
24 g3880.t1 ProSiteProfiles PS51057 Paired DNA-binding domain profile. 19 145 62.537
23 g3880.t1 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 182 242 20.617
16 g3880.t1 SMART SM00351 pax3 19 143 7.7E-87
17 g3880.t1 SMART SM00389 HOX_1 184 246 1.0E-25
10 g3880.t1 SUPERFAMILY SSF46689 Homeodomain-like 21 144 7.84E-42
9 g3880.t1 SUPERFAMILY SSF46689 Homeodomain-like 178 249 6.84E-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 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. There were no conditions that were differentially expressed