Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein gooseberry-neuro.

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 g3795 g3795.t1 TTS g3795.t1 27978053 27978053
chr_3 g3795 g3795.t1 isoform g3795.t1 27978104 27982307
chr_3 g3795 g3795.t1 exon g3795.t1.exon1 27978104 27978372
chr_3 g3795 g3795.t1 cds g3795.t1.CDS1 27978104 27978372
chr_3 g3795 g3795.t1 exon g3795.t1.exon2 27978426 27978737
chr_3 g3795 g3795.t1 cds g3795.t1.CDS2 27978426 27978737
chr_3 g3795 g3795.t1 exon g3795.t1.exon3 27978795 27978983
chr_3 g3795 g3795.t1 cds g3795.t1.CDS3 27978795 27978983
chr_3 g3795 g3795.t1 exon g3795.t1.exon4 27980883 27980994
chr_3 g3795 g3795.t1 cds g3795.t1.CDS4 27980883 27980994
chr_3 g3795 g3795.t1 exon g3795.t1.exon5 27981223 27981320
chr_3 g3795 g3795.t1 cds g3795.t1.CDS5 27981223 27981320
chr_3 g3795 g3795.t1 exon g3795.t1.exon6 27981414 27981629
chr_3 g3795 g3795.t1 cds g3795.t1.CDS6 27981414 27981629
chr_3 g3795 g3795.t1 exon g3795.t1.exon7 27982229 27982307
chr_3 g3795 g3795.t1 cds g3795.t1.CDS7 27982229 27982307
chr_3 g3795 g3795.t1 TSS g3795.t1 27982502 27982502

Sequences

>g3795.t1 Gene=g3795 Length=1275
ATGGATATATCAGGAACAATAAGTAATACAAGTGGCTCTCTAAATATGCGACCACTCTTT
GCTGGCTATCCATTTCAAGGACAAGGCAGAGTAAATCAACTTGGTGGAGTTTTCATTAAT
GGTAGACCACTACCTAATCATATAAGACTAAAAATTGTCGAAATGGCTGCATCAGGTGTG
AGACCTTGCGTAATTAGTCGACAATTAAGAGTTTCACATGGATGTGTTTCAAAAATTCTT
AATAGATATCAAGAAACAGGTAGCATTAGACCTGGAGTGATCGGTGGAAGCAAACCTCGT
GTTGCAACACCAGATATTGAAAATCGAATAGAAGAAATGAAAAAGGAAAATCCTGGAATT
TTCAGTTGGGAAATTAGAGAAAGATTGATAAAGGAAGGAGTTGTGGATCCACCGTCTGTG
AGCTCAATTTCAAGGTTGCTTCGTGGTGGCATTAGCGATAGAAAAGAAGATCGAAAGGAC
TATTCAATTCATGGAATTCTGGGTGGCCGAGGAACTGATTCAGATAGTGAAACGGAGAGT
GAACCTGGCATCGTATTAAAACGAAAACAACGAAGATCGCGTACAACTTTTTCTGGTGAT
CAACTTGAGGCTTTAGAGAAAGCATTTGCAAGAACTCAATATCCTGATGTTTATACAAGA
GAAGAACTTGCACAAAGTACCGGCCTTACTGAAGCGAGAATTCAAGTTTGGTTCTCAAAT
CGTCGTGCTCGATTAAGAAAGCATTCGGGAAATGGAGGAAGTATAAATATGGGCCCACCA
CCATTAGGATCAATTTCTCAATACCATCACTCTTCATCAATGTCAAATGAACCATATCAA
ATGATGAATGGCTATGATTTTCTTAATTCATCAGGTCCACATCATCATCAAAATTCATTT
TCATCATCAGCACTTGGAAATTTTCAACATTCGCCATTTGCTAATCAATCTCAAAATTTC
AATAATGTCACTACCGCTGCAGCTATGCATTTCAATCAAAATCAAGATTATATAACGTCT
AATAAACATATGAGTGAACCACATGAAGCGATAATAGCGAAACCTACAAATAGTCCAAAT
TCTTCATCACCACAAGGAATTACAAATGATCCAATATACTCAAAGCACCACATTGAAGTG
AGCAACAATTGGCCAACATCAAATTATCAATCACAGCAATACTCATTATCAAGCTTGTGT
CAGGCACCAGCACCAACAAATGTTCCATTAGATTATCACCAATCATATGCAAATTCAAAC
AAATATTGGTCTTAA

>g3795.t1 Gene=g3795 Length=424
MDISGTISNTSGSLNMRPLFAGYPFQGQGRVNQLGGVFINGRPLPNHIRLKIVEMAASGV
RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDIENRIEEMKKENPGI
FSWEIRERLIKEGVVDPPSVSSISRLLRGGISDRKEDRKDYSIHGILGGRGTDSDSETES
EPGIVLKRKQRRSRTTFSGDQLEALEKAFARTQYPDVYTREELAQSTGLTEARIQVWFSN
RRARLRKHSGNGGSINMGPPPLGSISQYHHSSSMSNEPYQMMNGYDFLNSSGPHHHQNSF
SSSALGNFQHSPFANQSQNFNNVTTAAAMHFNQNQDYITSNKHMSEPHEAIIAKPTNSPN
SSSPQGITNDPIYSKHHIEVSNNWPTSNYQSQQYSLSSLCQAPAPTNVPLDYHQSYANSN
KYWS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g3795.t1 CDD cd00131 PAX 27 149 1.70858E-77
17 g3795.t1 CDD cd00086 homeodomain 191 249 3.68185E-25
14 g3795.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 27 95 5.7E-38
15 g3795.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 96 157 4.3E-26
13 g3795.t1 Gene3D G3DSA:1.10.10.60 - 174 251 3.7E-29
22 g3795.t1 MobiDBLite mobidb-lite consensus disorder prediction 162 184 -
3 g3795.t1 PANTHER PTHR45636 PAIRED BOX PROTEIN PAX-6-RELATED-RELATED 13 397 1.8E-168
4 g3795.t1 PANTHER PTHR45636:SF3 PROTEIN GOOSEBERRY-RELATED 13 397 1.8E-168
6 g3795.t1 PRINTS PR00027 Paired box signature 31 46 1.2E-39
8 g3795.t1 PRINTS PR00027 Paired box signature 49 67 1.2E-39
5 g3795.t1 PRINTS PR00027 Paired box signature 69 86 1.2E-39
7 g3795.t1 PRINTS PR00027 Paired box signature 87 104 1.2E-39
9 g3795.t1 PRINTS PR00031 Lambda-repressor HTH signature 219 228 5.6E-5
10 g3795.t1 PRINTS PR00031 Lambda-repressor HTH signature 228 244 5.6E-5
2 g3795.t1 Pfam PF00292 ‘Paired box’ domain 27 148 7.4E-69
1 g3795.t1 Pfam PF00046 Homeodomain 191 247 3.0E-22
20 g3795.t1 ProSitePatterns PS00034 Paired DNA-binding domain signature. 61 77 -
21 g3795.t1 ProSitePatterns PS00027 ‘Homeobox’ domain signature. 223 246 -
24 g3795.t1 ProSiteProfiles PS51057 Paired DNA-binding domain profile. 27 150 60.872
23 g3795.t1 ProSiteProfiles PS50071 ‘Homeobox’ domain profile. 188 248 21.168
18 g3795.t1 SMART SM00351 pax3 27 148 5.2E-79
19 g3795.t1 SMART SM00389 HOX_1 190 252 1.2E-28
12 g3795.t1 SUPERFAMILY SSF46689 Homeodomain-like 29 148 5.97E-42
11 g3795.t1 SUPERFAMILY SSF46689 Homeodomain-like 184 249 3.85E-26

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.

Raw TPM values