General information for g5516.t1
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.t1 | isoform | g5516.t1 | 10029757 | 10032147 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon1 | 10029757 | 10029759 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS1 | 10029757 | 10029759 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon2 | 10029940 | 10030059 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS2 | 10029940 | 10030059 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon3 | 10030120 | 10030225 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS3 | 10030120 | 10030225 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon4 | 10030311 | 10030317 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS4 | 10030311 | 10030317 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon5 | 10030375 | 10030555 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS5 | 10030375 | 10030555 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon6 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS6 | 10030628 | 10030867 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon7 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS7 | 10030930 | 10031087 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon8 | 10031164 | 10031375 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS8 | 10031164 | 10031375 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon9 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS9 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon10 | 10031715 | 10031885 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS10 | 10031715 | 10031885 |
| chr_2 | g5516 | g5516.t1 | exon | g5516.t1.exon11 | 10031945 | 10032147 |
| chr_2 | g5516 | g5516.t1 | cds | g5516.t1.CDS11 | 10031945 | 10032147 |
| chr_2 | g5516 | g5516.t1 | TTS | g5516.t1 | 10032590 | 10032590 |
| chr_2 | g5516 | g5516.t1 | TSS | g5516.t1 | NA | NA |
Sequences
>g5516.t1 Gene=g5516 Length=1584
ATGAAAGAAAAGCAATCACAAGAGGTTGTTGAAAATGCATTGGGGGAGATGAAAAAGATC
TACAAATCGAAGTTATTGCCGCTCGAAGAACATTACAATTTTCATGATTTTCATTCACCA
AAGCTTGAAGATCCAGACTTTGATGCTAAACCGATGATTCTTTTAGTGGGGCAGTATTCA
ACTGGAAAAACAACTTTCATTCGATATTTACTAGAGAGAGATTTTCCTGGAATAAGAATT
GGGCCAGAGCCTACAACTGATCGCTTTATTGCGGTGATGTACGATGACAAAGAAGGTATT
ATTCCTGGAAATGCATTAGTTGTTGACCCTAAGAAACAATTTAGACCACTCAGCAAATAT
GGAAACGCCTTCTTAAATCGTTTCCAATGCTCAAGTGTTAATTCACCTGTATTGCAGGCT
ATTTCAATTGTTGACACTCCAGGTATTTTGAGCGGTGAAAAACAACGAGTTGATCGCGGT
TATGATTTTACTGGAGTACTTGAATGGTTTGCTGAACGAGTCGATCGCATTATTTTGCTT
TTTGATGCTCATAAGCTTGACATTTCCGATGAATTTAGACGATCAATTGAAGCACTTCGC
GGACATGATGATAAAATTAGAATTGTGCTAAATAAAGCGGATATGGTTGATCATCAGCAA
TTGATGCGTGTATATGGTGCATTAATGTGGTCACTTGGAAAAGTCTTACAAACACCCGAA
GTTGCTCGCGTGTATATTGGATCTTTTTGGGATCAACCTTTAAGATATGATGTTAATAGA
CGTCTTTTTGAAGATGAAGAACAAGATCTCTTTAGAGACTTACAATCACTGCCAAGAAAC
GCAGCTTTGCGTAAGCTAAATGATTTAATTAAAAGAGCAAGACTTGCAAAGGTGCACGCA
TACATAATTAGTGAATTAAGAAATGAGATGCCTTCAGTTTTTGGAAAAGACAGCAAGAAA
AAGGATCTCATTAAAAATATTGGAAATATTTATGATCGTCTTCAACGCGAGCATCAAATA
TCGCCAGGCGATTTTCCTGACATTAAGAAAATGCAAGAGGTTTTGGCAAATCAAGACTTT
TCAAAGTTCCATTCGCTTAAAATGCCCTTGTTAGAAACTGTAGATCGAATGCTTGCAAAT
GACATTGCTAGATTAATGAATTTGATTCCTCAAGAAGAAGCTGAGCTTGTTTCTGAACCT
TTGATTAAAGGAGGTGCCTTCCAAGGTATTGAAGATACCATATCACCATTTGGTTATAAA
CGCGGTGAAGGAATTGATGCTGGTTCTGGAGAAATTGATTGGATTTGTGAACGTGATAGA
GCACGTACTGATCCAATCTTTGAATCACTCAATCCTGTTGATGGAAAAATTAGTGGCGCT
GCCGCCAAGAGTGAATTGATCAAATCAAAATTACCTAATTCAGTACTTTCTAAAATCTGG
AAATTATCAGATGTTGATTGTGATGGTTTCCTGGATATTGAAGAATTTGCACTCGCTATG
CATTTAATAAATGTAAAAATTGACGGAAATGAATTGCCCAACATTTTACCGGATCATTTA
ATTCCACCATCACACAGAGTATGA
>g5516.t1 Gene=g5516 Length=527
MKEKQSQEVVENALGEMKKIYKSKLLPLEEHYNFHDFHSPKLEDPDFDAKPMILLVGQYS
TGKTTFIRYLLERDFPGIRIGPEPTTDRFIAVMYDDKEGIIPGNALVVDPKKQFRPLSKY
GNAFLNRFQCSSVNSPVLQAISIVDTPGILSGEKQRVDRGYDFTGVLEWFAERVDRIILL
FDAHKLDISDEFRRSIEALRGHDDKIRIVLNKADMVDHQQLMRVYGALMWSLGKVLQTPE
VARVYIGSFWDQPLRYDVNRRLFEDEEQDLFRDLQSLPRNAALRKLNDLIKRARLAKVHA
YIISELRNEMPSVFGKDSKKKDLIKNIGNIYDRLQREHQISPGDFPDIKKMQEVLANQDF
SKFHSLKMPLLETVDRMLANDIARLMNLIPQEEAELVSEPLIKGGAFQGIEDTISPFGYK
RGEGIDAGSGEIDWICERDRARTDPIFESLNPVDGKISGAAAKSELIKSKLPNSVLSKIW
KLSDVDCDGFLDIEEFALAMHLINVKIDGNELPNILPDHLIPPSHRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5516.t1 | CDD | cd09913 | EHD | 52 | 292 | 1.92483E-165 |
| 13 | g5516.t1 | CDD | cd00052 | EH | 446 | 506 | 9.03982E-24 |
| 10 | g5516.t1 | Gene3D | G3DSA:1.10.268.20 | - | 16 | 378 | 2.3E-164 |
| 9 | g5516.t1 | Gene3D | G3DSA:3.40.50.300 | - | 53 | 277 | 2.3E-164 |
| 11 | g5516.t1 | Gene3D | G3DSA:1.10.238.10 | - | 426 | 527 | 6.8E-31 |
| 5 | g5516.t1 | PANTHER | PTHR11216:SF57 | EH DOMAIN-CONTAINING PROTEIN 4 | 7 | 526 | 5.2E-253 |
| 6 | g5516.t1 | PANTHER | PTHR11216 | EH DOMAIN | 7 | 526 | 5.2E-253 |
| 2 | g5516.t1 | Pfam | PF16880 | N-terminal EH-domain containing protein | 17 | 48 | 1.6E-15 |
| 4 | g5516.t1 | Pfam | PF00350 | Dynamin family | 53 | 212 | 1.6E-14 |
| 1 | g5516.t1 | Pfam | PF18150 | Domain of unknown function (DUF5600) | 280 | 386 | 5.6E-45 |
| 3 | g5516.t1 | Pfam | PF12763 | Cytoskeletal-regulatory complex EF hand | 445 | 525 | 2.1E-18 |
| 14 | g5516.t1 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 484 | 496 | - |
| 16 | g5516.t1 | ProSiteProfiles | PS51718 | Dynamin-type guanine nucleotide-binding (G) domain profile. | 47 | 278 | 39.446 |
| 17 | g5516.t1 | ProSiteProfiles | PS50031 | EH domain profile. | 439 | 527 | 23.373 |
| 18 | g5516.t1 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 471 | 506 | 12.31 |
| 15 | g5516.t1 | SMART | SM00027 | eh_3 | 432 | 526 | 3.6E-37 |
| 7 | g5516.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 40 | 299 | 1.49E-32 |
| 8 | g5516.t1 | SUPERFAMILY | SSF47473 | EF-hand | 432 | 526 | 4.46E-24 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5516/g5516.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t1.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 transcript has been annotated with K12483 (EH domain-containing protein 1)
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.
