General information for g5516.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as EH domain-containing protein 1.
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.t13 | isoform | g5516.t13 | 10029757 | 10032582 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon1 | 10029757 | 10030225 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon2 | 10030375 | 10030555 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS1 | 10030415 | 10030555 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon3 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS2 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon4 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS3 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon5 | 10031164 | 10031375 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS4 | 10031164 | 10031375 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon6 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS5 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon7 | 10031718 | 10031885 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS6 | 10031718 | 10031885 |
| chr_2 | g5516 | g5516.t13 | exon | g5516.t13.exon8 | 10031945 | 10032582 |
| chr_2 | g5516 | g5516.t13 | cds | g5516.t13.CDS7 | 10031945 | 10032147 |
| chr_2 | g5516 | g5516.t13 | TTS | g5516.t13 | 10032590 | 10032590 |
| chr_2 | g5516 | g5516.t13 | TSS | g5516.t13 | NA | NA |
Sequences
>g5516.t13 Gene=g5516 Length=2249
ATGGTAAGAAAGACTTTATTGCTTACAAAACTCTGAAGAGAAGGGCGCTTTCAACTCTTG
TGATTTTTTTATTGCTTTGAAGTTTTCACTTGAGTAGTTTTTGGCTGCGTTGTTCATGTT
CTTAATTTTTAATTCGAGTCTTAAGTAAAAATTTATTAAATTAAAATGTTTTCTTGGCTA
AAGAAAGAAAAGCAATCACAAGAGGTTGTTGAAAATGCATTGGGGGAGATGAAAAAGATC
TACAAATCGAAGTTATTGCCGCTCGAAGAACATTACAATTTTCATGATTTTCATTCACCA
AAGGTAATGATGATAATAAGTACTAAGCAGTTCATATATTATTCAATCAATTTCATTATC
TAGCTTGAAGATCCAGACTTTGATGCTAAACCGATGATTCTTTTAGTGGGGCAGTATTCA
ACTGGAAAAACAACTTTCATTCGATATTTACTAGAGAGAGATTTTCCTGAATTGGGCCAG
AGCCTACAACTGATCGCTTTATTGCGGTGATGTACGATGACAAAGAAGGTATTATTCCTG
GAAATGCATTAGTTGTTGACCCTAAGAAACAATTTAGACCACTCAGCAAATATGGAAACG
CCTTCTTAAATCGTTTCCAATGCTCAAGTGTTAATTCACCTGTATTGCAGGCTATTTCAA
TTGTTGACACTCCAGGTATTTTGAGCGGTGAAAAACAACGAGTTGATCGCGGTTATGATT
TTACTGGAGTACTTGAATGGTTTGCTGAACGAGTCGATCGCATTATTTTGCTTTTTGATG
CTCATAAGCTTGACATTTCCGATGAATTTAGACGATCAATTGAAGCACTTCGCGGACATG
ATGATAAAATTAGAATTGTGCTAAATAAAGCGGATATGGTTGATCATCAGCAATTGATGC
GTGTATATGGTGCATTAATGTGGTCACTTGGAAAAGTCTTACAAACACCCGAAGTTGCTC
GCGTGTATATTGGATCTTTTTGGGATCAACCTTTAAGATATGATGTTAATAGACGTCTTT
TTGAAGATGAAGAACAAGATCTCTTTAGAGACTTACAATCACTGCCAAGAAACGCAGCTT
TGCGTAAGCTAAATGATTTAATTAAAAGAGCAAGACTTGCAAAGGTGCACGCATACATAA
TTAGTGAATTAAGAAATGAGATGCCTTCAGTTTTTGGAAAAGACAGCAAGAAAAAGGATC
TCATTAAAAATATTGGAAATATTTATGATCGTCTTCAACGCGAGCATCAAATATCGCCAG
GCGATTTTCCTGACATTAAGAAAATGCAAGAGGTTTTGGCAAATCAAGACTTTTCAAAGT
TCCATTCGCTTAAAATGCCCTTGTTAGAAACTGTAGATCGAATGCTTGCAAATGACATTG
CTAGATTAATGAATTTGATTCCTCAAGAAGAAGCTGAGCTTGTTTCTGAACCTTTGATTA
AAGGTGCCTTCCAAGGTATTGAAGATACCATATCACCATTTGGTTATAAACGCGGTGAAG
GAATTGATGCTGGTTCTGGAGAAATTGATTGGATTTGTGAACGTGATAGAGCACGTACTG
ATCCAATCTTTGAATCACTCAATCCTGTTGATGGAAAAATTAGTGGCGCTGCCGCCAAGA
GTGAATTGATCAAATCAAAATTACCTAATTCAGTACTTTCTAAAATCTGGAAATTATCAG
ATGTTGATTGTGATGGTTTCCTGGATATTGAAGAATTTGCACTCGCTATGCATTTAATAA
ATGTAAAAATTGACGGAAATGAATTGCCCAACATTTTACCGGATCATTTAATTCCACCAT
CACACAGAGTATGAACATTGTCGTTGACATTCATCATAATTTGCACATCACAGTTATAAT
CACTTTTGTTAGTAACAATTTCCTTCTATCATCTTTATGAATGTGAAAATGTCAACTAAT
CATTTGTGTGCATCACTTGAGTAATTTTCTACTTGGAGAAAAATATATATATATTTTTTG
ATCAAAAATCATCCAAACGACAACAATGGACAAATCATCCTTTTTTTTGAATTTAGAACC
ACACGGGCTTATTTTCTTCCTTCCTTAGTAAAATTCAATACGCATATTATATACTTTAAA
ATAAAGAAAGAAACAATTCATATAGTTTACAGTTTACTCTTATATAAGATATACACCCTA
AATATTATTATTATATTATATACACATATTTTATTAAAATACCATTTTGAATTATTTATA
AATTTATGAATAATAAAGTTCACAAAATG
>g5516.t13 Gene=g5516 Length=434
MYDDKEGIIPGNALVVDPKKQFRPLSKYGNAFLNRFQCSSVNSPVLQAISIVDTPGILSG
EKQRVDRGYDFTGVLEWFAERVDRIILLFDAHKLDISDEFRRSIEALRGHDDKIRIVLNK
ADMVDHQQLMRVYGALMWSLGKVLQTPEVARVYIGSFWDQPLRYDVNRRLFEDEEQDLFR
DLQSLPRNAALRKLNDLIKRARLAKVHAYIISELRNEMPSVFGKDSKKKDLIKNIGNIYD
RLQREHQISPGDFPDIKKMQEVLANQDFSKFHSLKMPLLETVDRMLANDIARLMNLIPQE
EAELVSEPLIKGAFQGIEDTISPFGYKRGEGIDAGSGEIDWICERDRARTDPIFESLNPV
DGKISGAAAKSELIKSKLPNSVLSKIWKLSDVDCDGFLDIEEFALAMHLINVKIDGNELP
NILPDHLIPPSHRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5516.t13 | CDD | cd09913 | EHD | 1 | 200 | 4.44045E-133 |
| 11 | g5516.t13 | CDD | cd00052 | EH | 353 | 413 | 9.48545E-24 |
| 7 | g5516.t13 | Gene3D | G3DSA:3.40.50.300 | - | 2 | 185 | 4.8E-119 |
| 8 | g5516.t13 | Gene3D | G3DSA:1.10.268.20 | - | 186 | 298 | 4.8E-119 |
| 9 | g5516.t13 | Gene3D | G3DSA:1.10.238.10 | - | 333 | 434 | 4.9E-31 |
| 3 | g5516.t13 | PANTHER | PTHR11216:SF57 | EH DOMAIN-CONTAINING PROTEIN 4 | 1 | 433 | 1.8E-202 |
| 4 | g5516.t13 | PANTHER | PTHR11216 | EH DOMAIN | 1 | 433 | 1.8E-202 |
| 1 | g5516.t13 | Pfam | PF18150 | Domain of unknown function (DUF5600) | 188 | 294 | 4.0E-45 |
| 2 | g5516.t13 | Pfam | PF12763 | Cytoskeletal-regulatory complex EF hand | 352 | 432 | 1.5E-18 |
| 12 | g5516.t13 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 391 | 403 | - |
| 14 | g5516.t13 | ProSiteProfiles | PS51718 | Dynamin-type guanine nucleotide-binding (G) domain profile. | 1 | 186 | 28.346 |
| 15 | g5516.t13 | ProSiteProfiles | PS50031 | EH domain profile. | 346 | 434 | 23.373 |
| 16 | g5516.t13 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 378 | 413 | 12.31 |
| 13 | g5516.t13 | SMART | SM00027 | eh_3 | 339 | 433 | 3.6E-37 |
| 5 | g5516.t13 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 3 | 207 | 2.1E-19 |
| 6 | g5516.t13 | SUPERFAMILY | SSF47473 | EF-hand | 339 | 433 | 3.24E-24 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5516/g5516.t13; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t13.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 |
| 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.
