General information for g5516.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as EH domain-containing protein 3.
Parent gene
- The parent gene g5516 is located on chr_2: 10031743..10032883 (+ strand)
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.t4 | isoform | g5516.t4 | 10029757 | 10031365 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon1 | 10029757 | 10030059 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon2 | 10030120 | 10030229 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon3 | 10030371 | 10030555 |
| chr_2 | g5516 | g5516.t4 | cds | g5516.t4.CDS1 | 10030415 | 10030555 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon4 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t4 | cds | g5516.t4.CDS2 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon5 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t4 | cds | g5516.t4.CDS3 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t4 | exon | g5516.t4.exon6 | 10031164 | 10031365 |
| chr_2 | g5516 | g5516.t4 | cds | g5516.t4.CDS4 | 10031164 | 10031365 |
| chr_2 | g5516 | g5516.t4 | TSS | g5516.t4 | NA | NA |
| chr_2 | g5516 | g5516.t4 | TTS | g5516.t4 | NA | NA |
Sequences
>g5516.t4 Gene=g5516 Length=1198
ATGGTAAGAAAGACTTTATTGCTTACAAAACTCTGAAGAGAAGGGCGCTTTCAACTCTTG
TGATTTTTTTATTGCTTTGAAGTTTTCACTTGAGTAGTTTTTGGCTGCGTTGTTCATGTT
CTTAATTTTTAATTCGAGTCTTAAGTAAAAATTTATTAAATTAAAATGTTTTCTTGGCTA
AAGAAAGAAAAGCAATCACAAGAGGTTGTTGAAAATGCATTGGGGGAGATGAAAAAGATC
TACAAATCGAAGTTATTGCCGCTCGAAGAACATTACAATTTTCATGATTTTCATTCACCA
AAGCTTGAAGATCCAGACTTTGATGCTAAACCGATGATTCTTTTAGTGGGGCAGTATTCA
ACTGGAAAAACAACTTTCATTCGATATTTACTAGAGAGAGATTTTCCTGGTAATAAGAAT
TGGGCCAGAGCCTACAACTGATCGCTTTATTGCGGTGATGTACGATGACAAAGAAGGTAT
TATTCCTGGAAATGCATTAGTTGTTGACCCTAAGAAACAATTTAGACCACTCAGCAAATA
TGGAAACGCCTTCTTAAATCGTTTCCAATGCTCAAGTGTTAATTCACCTGTATTGCAGGC
TATTTCAATTGTTGACACTCCAGGTATTTTGAGCGGTGAAAAACAACGAGTTGATCGCGG
TTATGATTTTACTGGAGTACTTGAATGGTTTGCTGAACGAGTCGATCGCATTATTTTGCT
TTTTGATGCTCATAAGCTTGACATTTCCGATGAATTTAGACGATCAATTGAAGCACTTCG
CGGACATGATGATAAAATTAGAATTGTGCTAAATAAAGCGGATATGGTTGATCATCAGCA
ATTGATGCGTGTATATGGTGCATTAATGTGGTCACTTGGAAAAGTCTTACAAACACCCGA
AGTTGCTCGCGTGTATATTGGATCTTTTTGGGATCAACCTTTAAGATATGATGTTAATAG
ACGTCTTTTTGAAGATGAAGAACAAGATCTCTTTAGAGACTTACAATCACTGCCAAGAAA
CGCAGCTTTGCGTAAGCTAAATGATTTAATTAAAAGAGCAAGACTTGCAAAGGTGCACGC
ATACATAATTAGTGAATTAAGAAATGAGATGCCTTCAGTTTTTGGAAAAGACAGCAAGAA
AAAGGATCTCATTAAAAATATTGGAAATATTTATGATCGTCTTCAACGCGAGCATCAA
>g5516.t4 Gene=g5516 Length=247
MYDDKEGIIPGNALVVDPKKQFRPLSKYGNAFLNRFQCSSVNSPVLQAISIVDTPGILSG
EKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNK
ADMVDHQQLMRVYGALMWSLGKVLQTPEVARVYIGSFWDQPLRYDVNRRLFEDEEQDLFR
DLQSLPRNAALRKLNDLIKRARLAKVHAYIISELRNEMPSVFGKDSKKKDLIKNIGNIYD
RLQREHQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5516.t4 | CDD | cd09913 | EHD | 1 | 200 | 0.000 |
| 5 | g5516.t4 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 196 | 0.000 |
| 2 | g5516.t4 | PANTHER | PTHR11216:SF57 | EH DOMAIN-CONTAINING PROTEIN 4 | 1 | 247 | 0.000 |
| 3 | g5516.t4 | PANTHER | PTHR11216 | EH DOMAIN | 1 | 247 | 0.000 |
| 1 | g5516.t4 | Pfam | PF18150 | Domain of unknown function (DUF5600) | 188 | 247 | 0.000 |
| 6 | g5516.t4 | ProSiteProfiles | PS51718 | Dynamin-type guanine nucleotide-binding (G) domain profile. | 1 | 186 | 28.346 |
| 4 | g5516.t4 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 207 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5516/g5516.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0032456 | endocytic recycling | BP |
| GO:0005525 | GTP binding | MF |
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.
