Gene loci information

Transcript annotation

  • This transcript has been annotated as EH domain-containing protein 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_2 g5516 g5516.t12 isoform g5516.t12 10029757 10032582
chr_2 g5516 g5516.t12 exon g5516.t12.exon1 10029757 10030059
chr_2 g5516 g5516.t12 exon g5516.t12.exon2 10030120 10030225
chr_2 g5516 g5516.t12 exon g5516.t12.exon3 10030375 10030555
chr_2 g5516 g5516.t12 exon g5516.t12.exon4 10030628 10030867
chr_2 g5516 g5516.t12 exon g5516.t12.exon5 10030928 10031087
chr_2 g5516 g5516.t12 cds g5516.t12.CDS1 10030936 10031087
chr_2 g5516 g5516.t12 exon g5516.t12.exon6 10031164 10031375
chr_2 g5516 g5516.t12 cds g5516.t12.CDS2 10031164 10031375
chr_2 g5516 g5516.t12 exon g5516.t12.exon7 10031473 10031655
chr_2 g5516 g5516.t12 cds g5516.t12.CDS3 10031473 10031655
chr_2 g5516 g5516.t12 exon g5516.t12.exon8 10031715 10031885
chr_2 g5516 g5516.t12 cds g5516.t12.CDS4 10031715 10031885
chr_2 g5516 g5516.t12 exon g5516.t12.exon9 10031945 10032582
chr_2 g5516 g5516.t12 cds g5516.t12.CDS5 10031945 10032147
chr_2 g5516 g5516.t12 TTS g5516.t12 10032590 10032590
chr_2 g5516 g5516.t12 TSS g5516.t12 NA NA

Sequences

>g5516.t12 Gene=g5516 Length=2194
ATGGTAAGAAAGACTTTATTGCTTACAAAACTCTGAAGAGAAGGGCGCTTTCAACTCTTG
TGATTTTTTTATTGCTTTGAAGTTTTCACTTGAGTAGTTTTTGGCTGCGTTGTTCATGTT
CTTAATTTTTAATTCGAGTCTTAAGTAAAAATTTATTAAATTAAAATGTTTTCTTGGCTA
AAGAAAGAAAAGCAATCACAAGAGGTTGTTGAAAATGCATTGGGGGAGATGAAAAAGATC
TACAAATCGAAGTTATTGCCGCTCGAAGAACATTACAATTTTCATGATTTTCATTCACCA
AAGCTTGAAGATCCAGACTTTGATGCTAAACCGATGATTCTTTTAGTGGGGCAGTATTCA
ACTGGAAAAACAACTTTCATTCGATATTTACTAGAGAGAGATTTTCCTGAATTGGGCCAG
AGCCTACAACTGATCGCTTTATTGCGGTGATGTACGATGACAAAGAAGGTATTATTCCTG
GAAATGCATTAGTTGTTGACCCTAAGAAACAATTTAGACCACTCAGCAAATATGGAAACG
CCTTCTTAAATCGTTTCCAATGCTCAAGTGTTAATTCACCTGTATTGCAGGCTATTTCAA
TTGTTGACACTCCAGGTATTTTGAGCGGTGAAAAACAACGAGTTGATCGCGGTTATGATT
TTACTGGAGTACTTGAATGGTTTGCTGAACGAGTCGATCGCATTATTTTGCTTTTTGATG
CTCATAAGCTTGACATTTCCGATGAATTTAGACGATCAATTGAAGCACTTCGCGGACATG
ATGATAAAATTAGAATTGTGCTAAATAAAGCGGATATGGTTGATCATCAGAGCAATTGAT
GCGTGTATATGGTGCATTAATGTGGTCACTTGGAAAAGTCTTACAAACACCCGAAGTTGC
TCGCGTGTATATTGGATCTTTTTGGGATCAACCTTTAAGATATGATGTTAATAGACGTCT
TTTTGAAGATGAAGAACAAGATCTCTTTAGAGACTTACAATCACTGCCAAGAAACGCAGC
TTTGCGTAAGCTAAATGATTTAATTAAAAGAGCAAGACTTGCAAAGGTGCACGCATACAT
AATTAGTGAATTAAGAAATGAGATGCCTTCAGTTTTTGGAAAAGACAGCAAGAAAAAGGA
TCTCATTAAAAATATTGGAAATATTTATGATCGTCTTCAACGCGAGCATCAAATATCGCC
AGGCGATTTTCCTGACATTAAGAAAATGCAAGAGGTTTTGGCAAATCAAGACTTTTCAAA
GTTCCATTCGCTTAAAATGCCCTTGTTAGAAACTGTAGATCGAATGCTTGCAAATGACAT
TGCTAGATTAATGAATTTGATTCCTCAAGAAGAAGCTGAGCTTGTTTCTGAACCTTTGAT
TAAAGGAGGTGCCTTCCAAGGTATTGAAGATACCATATCACCATTTGGTTATAAACGCGG
TGAAGGAATTGATGCTGGTTCTGGAGAAATTGATTGGATTTGTGAACGTGATAGAGCACG
TACTGATCCAATCTTTGAATCACTCAATCCTGTTGATGGAAAAATTAGTGGCGCTGCCGC
CAAGAGTGAATTGATCAAATCAAAATTACCTAATTCAGTACTTTCTAAAATCTGGAAATT
ATCAGATGTTGATTGTGATGGTTTCCTGGATATTGAAGAATTTGCACTCGCTATGCATTT
AATAAATGTAAAAATTGACGGAAATGAATTGCCCAACATTTTACCGGATCATTTAATTCC
ACCATCACACAGAGTATGAACATTGTCGTTGACATTCATCATAATTTGCACATCACAGTT
ATAATCACTTTTGTTAGTAACAATTTCCTTCTATCATCTTTATGAATGTGAAAATGTCAA
CTAATCATTTGTGTGCATCACTTGAGTAATTTTCTACTTGGAGAAAAATATATATATATT
TTTTGATCAAAAATCATCCAAACGACAACAATGGACAAATCATCCTTTTTTTTGAATTTA
GAACCACACGGGCTTATTTTCTTCCTTCCTTAGTAAAATTCAATACGCATATTATATACT
TTAAAATAAAGAAAGAAACAATTCATATAGTTTACAGTTTACTCTTATATAAGATATACA
CCCTAAATATTATTATTATATTATATACACATATTTTATTAAAATACCATTTTGAATTAT
TTATAAATTTATGAATAATAAAGTTCACAAAATG

>g5516.t12 Gene=g5516 Length=306
MRVYGALMWSLGKVLQTPEVARVYIGSFWDQPLRYDVNRRLFEDEEQDLFRDLQSLPRNA
ALRKLNDLIKRARLAKVHAYIISELRNEMPSVFGKDSKKKDLIKNIGNIYDRLQREHQIS
PGDFPDIKKMQEVLANQDFSKFHSLKMPLLETVDRMLANDIARLMNLIPQEEAELVSEPL
IKGGAFQGIEDTISPFGYKRGEGIDAGSGEIDWICERDRARTDPIFESLNPVDGKISGAA
AKSELIKSKLPNSVLSKIWKLSDVDCDGFLDIEEFALAMHLINVKIDGNELPNILPDHLI
PPSHRV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5516.t12 CDD cd00052 EH 225 285 1.48345E-24
6 g5516.t12 Gene3D G3DSA:1.10.268.20 - 33 174 3.9E-55
7 g5516.t12 Gene3D G3DSA:1.10.238.10 - 205 306 2.6E-31
3 g5516.t12 PANTHER PTHR11216:SF57 EH DOMAIN-CONTAINING PROTEIN 4 1 305 1.0E-125
4 g5516.t12 PANTHER PTHR11216 EH DOMAIN 1 305 1.0E-125
1 g5516.t12 Pfam PF18150 Domain of unknown function (DUF5600) 59 165 2.0E-45
2 g5516.t12 Pfam PF12763 Cytoskeletal-regulatory complex EF hand 224 304 8.2E-19
9 g5516.t12 ProSitePatterns PS00018 EF-hand calcium-binding domain. 263 275 -
11 g5516.t12 ProSiteProfiles PS50031 EH domain profile. 218 306 23.373
12 g5516.t12 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 250 285 12.31
10 g5516.t12 SMART SM00027 eh_3 211 305 3.6E-37
5 g5516.t12 SUPERFAMILY SSF47473 EF-hand 211 305 1.62E-24

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5516/g5516.t12; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t12.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0005509 calcium ion binding MF
GO:0032456 endocytic recycling BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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