General information for g5516.t15
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.t15 | isoform | g5516.t15 | 10031079 | 10032582 |
| chr_2 | g5516 | g5516.t15 | exon | g5516.t15.exon1 | 10031079 | 10031087 |
| chr_2 | g5516 | g5516.t15 | exon | g5516.t15.exon2 | 10031164 | 10031375 |
| chr_2 | g5516 | g5516.t15 | cds | g5516.t15.CDS1 | 10031276 | 10031375 |
| chr_2 | g5516 | g5516.t15 | exon | g5516.t15.exon3 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t15 | cds | g5516.t15.CDS2 | 10031473 | 10031655 |
| chr_2 | g5516 | g5516.t15 | exon | g5516.t15.exon4 | 10031715 | 10031885 |
| chr_2 | g5516 | g5516.t15 | cds | g5516.t15.CDS3 | 10031715 | 10031885 |
| chr_2 | g5516 | g5516.t15 | exon | g5516.t15.exon5 | 10031945 | 10032582 |
| chr_2 | g5516 | g5516.t15 | cds | g5516.t15.CDS4 | 10031945 | 10032147 |
| chr_2 | g5516 | g5516.t15 | TTS | g5516.t15 | 10032590 | 10032590 |
| chr_2 | g5516 | g5516.t15 | TSS | g5516.t15 | NA | NA |
Sequences
>g5516.t15 Gene=g5516 Length=1213
TCTCTTTAGAGACTTACAATCACTGCCAAGAAACGCAGCTTTGCGTAAGCTAAATGATTT
AATTAAAAGAGCAAGACTTGCAAAGGTGCACGCATACATAATTAGTGAATTAAGAAATGA
GATGCCTTCAGTTTTTGGAAAAGACAGCAAGAAAAAGGATCTCATTAAAAATATTGGAAA
TATTTATGATCGTCTTCAACGCGAGCATCAAATATCGCCAGGCGATTTTCCTGACATTAA
GAAAATGCAAGAGGTTTTGGCAAATCAAGACTTTTCAAAGTTCCATTCGCTTAAAATGCC
CTTGTTAGAAACTGTAGATCGAATGCTTGCAAATGACATTGCTAGATTAATGAATTTGAT
TCCTCAAGAAGAAGCTGAGCTTGTTTCTGAACCTTTGATTAAAGGAGGTGCCTTCCAAGG
TATTGAAGATACCATATCACCATTTGGTTATAAACGCGGTGAAGGAATTGATGCTGGTTC
TGGAGAAATTGATTGGATTTGTGAACGTGATAGAGCACGTACTGATCCAATCTTTGAATC
ACTCAATCCTGTTGATGGAAAAATTAGTGGCGCTGCCGCCAAGAGTGAATTGATCAAATC
AAAATTACCTAATTCAGTACTTTCTAAAATCTGGAAATTATCAGATGTTGATTGTGATGG
TTTCCTGGATATTGAAGAATTTGCACTCGCTATGCATTTAATAAATGTAAAAATTGACGG
AAATGAATTGCCCAACATTTTACCGGATCATTTAATTCCACCATCACACAGAGTATGAAC
ATTGTCGTTGACATTCATCATAATTTGCACATCACAGTTATAATCACTTTTGTTAGTAAC
AATTTCCTTCTATCATCTTTATGAATGTGAAAATGTCAACTAATCATTTGTGTGCATCAC
TTGAGTAATTTTCTACTTGGAGAAAAATATATATATATTTTTTGATCAAAAATCATCCAA
ACGACAACAATGGACAAATCATCCTTTTTTTTGAATTTAGAACCACACGGGCTTATTTTC
TTCCTTCCTTAGTAAAATTCAATACGCATATTATATACTTTAAAATAAAGAAAGAAACAA
TTCATATAGTTTACAGTTTACTCTTATATAAGATATACACCCTAAATATTATTATTATAT
TATATACACATATTTTATTAAAATACCATTTTGAATTATTTATAAATTTATGAATAATAA
AGTTCACAAAATG
>g5516.t15 Gene=g5516 Length=218
MPSVFGKDSKKKDLIKNIGNIYDRLQREHQISPGDFPDIKKMQEVLANQDFSKFHSLKMP
LLETVDRMLANDIARLMNLIPQEEAELVSEPLIKGGAFQGIEDTISPFGYKRGEGIDAGS
GEIDWICERDRARTDPIFESLNPVDGKISGAAAKSELIKSKLPNSVLSKIWKLSDVDCDG
FLDIEEFALAMHLINVKIDGNELPNILPDHLIPPSHRV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5516.t15 | CDD | cd00052 | EH | 137 | 197 | 2.58413E-25 |
| 6 | g5516.t15 | Gene3D | G3DSA:1.10.268.20 | - | 1 | 86 | 2.8E-31 |
| 7 | g5516.t15 | Gene3D | G3DSA:1.10.238.10 | - | 117 | 218 | 1.2E-31 |
| 3 | g5516.t15 | PANTHER | PTHR11216:SF57 | EH DOMAIN-CONTAINING PROTEIN 4 | 1 | 217 | 3.5E-72 |
| 4 | g5516.t15 | PANTHER | PTHR11216 | EH DOMAIN | 1 | 217 | 3.5E-72 |
| 1 | g5516.t15 | Pfam | PF18150 | Domain of unknown function (DUF5600) | 1 | 77 | 2.3E-26 |
| 2 | g5516.t15 | Pfam | PF12763 | Cytoskeletal-regulatory complex EF hand | 136 | 216 | 4.0E-19 |
| 9 | g5516.t15 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 175 | 187 | - |
| 11 | g5516.t15 | ProSiteProfiles | PS50031 | EH domain profile. | 130 | 218 | 23.373 |
| 12 | g5516.t15 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 162 | 197 | 12.31 |
| 10 | g5516.t15 | SMART | SM00027 | eh_3 | 123 | 217 | 3.6E-37 |
| 5 | g5516.t15 | SUPERFAMILY | SSF47473 | EF-hand | 123 | 217 | 7.8E-25 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5516/g5516.t15; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5516.t15.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