General information for g5478.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5478 is located on chr_2: 9810267..9819560 (- 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 | g5478 | g5478.t3 | isoform | g5478.t3 | 9805269 | 9806850 |
| chr_2 | g5478 | g5478.t3 | exon | g5478.t3.exon1 | 9805269 | 9805879 |
| chr_2 | g5478 | g5478.t3 | TTS | g5478.t3 | 9805274 | 9805274 |
| chr_2 | g5478 | g5478.t3 | cds | g5478.t3.CDS1 | 9805787 | 9805879 |
| chr_2 | g5478 | g5478.t3 | exon | g5478.t3.exon2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t3 | cds | g5478.t3.CDS2 | 9805939 | 9806049 |
| chr_2 | g5478 | g5478.t3 | exon | g5478.t3.exon3 | 9806112 | 9806850 |
| chr_2 | g5478 | g5478.t3 | cds | g5478.t3.CDS3 | 9806112 | 9806828 |
| chr_2 | g5478 | g5478.t3 | TSS | g5478.t3 | NA | NA |
Sequences
>g5478.t3 Gene=g5478 Length=1461
CAACATAAAAGAGATTATTGAAATGTTTGGATCACATCTAAATATCGATTTACAACAACG
TGGTGTTGAGTTTACACAACTTTTTGGTCCATATAAACATCTAAGAGAATCACTACTCGA
GAAAATGCCAGCAATGACTATTAATAGAATAAATGGCGCAAATTCAAATGGTGAAATGAT
TGGTGAAGGGGAAGTGATAAGGAGCAATAGTAGTGATAAAGTTGTGAACAATGGAAATAT
TCGATCAAATACAGATACATTACTTGATTTGCTTGGTTCTGGTGATGATATCATTTCATC
ATCATCATTCACTATTCCGACATCAACCCCGGCTCCAGCTGCAACAAACAATTTACTAGA
TCTTCTTGGCGATATTGACCTAGGTGCACCAACTATATCTGTTAATAATAATAATAACAA
TAATAACAGTGCAACATCTCCTATAACAATGTCTATCCTTGACGATAACGAGAACACGAA
AATTCCCGATGTTACAACAATGTTCAACATTAATGGTAGCAGCGGTGGTAATGCTCAAGC
AAATAATAGCAATTATGACCTGGGAGATTTTCTTTCATCGCCGACTTTACACAATACTAG
CGCAAAAATTATTACTGTTTTTGATAAGAATGATTTAGTTATTACGTTTGCAACATCAAG
GCACAATGATGACTATATCGAAGTTTTGATGTCGACAACCAATAATTCAATGGATACATT
AGAACAGTATTTATTTCAGGCTGCAGTTCCTAAAAGCTTTCAATTACAAATGATGTCACC
TACAGGCTCCGTCCTTTTGCCTGGTGGTGTTATTACACAAGAAATGCGTGTTAGAAGCAA
TTCGCCAAGTGCCGTCCTAAGAATGAAATTGAGAATTTCTTTTGTGTGTAATGGAAACCC
AATCTTGGAGCAAGCTGAAGTTAGCAATTTTCCTGATGTTTAATATCGACTGTCGACAAG
CGTTTAGATAACATTGAAGATGATTTAAAGTAATCTGTGTTTAGATAATGAAGCATTTTT
TATCTGTTGCTGTGCTTCTCTTGTAGAATGATATATTTCATTTATTCTGTCCTCATTTAT
TTTAACATATAGATAATTATTGATTATCAGAAAATATAATTTTACTACCTTTTGAAAATA
TATTGTTAAAGAGTAAAGTTTCTACTTATAATATATTATTTTAGATATAGACATACACTA
TTTTTTGTTTTGTAAATGATAAAAGACATTATTATCAAACAAAATTAGGAAGACACTACT
AATTTGTTTATTTTAATAATTTGCAAATTTATTGCTTTGATTTTGTACTTAATCATGCAT
TCAAGAAAAAAAATTATTCTAAAAGCATCATTGTCGTCTTCATCACTTTTTTTAAAAATA
AAGATATGGCGATTAAAATGTTTATTTCTTTAATGTATAAAAATAATTGATGAATAAAAT
TATTTCAAGTTTTACTAAAAA
>g5478.t3 Gene=g5478 Length=306
MFGSHLNIDLQQRGVEFTQLFGPYKHLRESLLEKMPAMTINRINGANSNGEMIGEGEVIR
SNSSDKVVNNGNIRSNTDTLLDLLGSGDDIISSSSFTIPTSTPAPAATNNLLDLLGDIDL
GAPTISVNNNNNNNNSATSPITMSILDDNENTKIPDVTTMFNINGSSGGNAQANNSNYDL
GDFLSSPTLHNTSAKIITVFDKNDLVITFATSRHNDDYIEVLMSTTNNSMDTLEQYLFQA
AVPKSFQLQMMSPTGSVLLPGGVITQEMRVRSNSPSAVLRMKLRISFVCNGNPILEQAEV
SNFPDV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5478.t3 | Gene3D | G3DSA:2.60.40.1230 | - | 192 | 306 | 0.000 |
| 2 | g5478.t3 | PANTHER | PTHR22780:SF5 | AP-1 COMPLEX SUBUNIT GAMMA | 3 | 304 | 0.000 |
| 3 | g5478.t3 | PANTHER | PTHR22780 | ADAPTIN, ALPHA/GAMMA/EPSILON | 3 | 304 | 0.000 |
| 1 | g5478.t3 | Pfam | PF02883 | Adaptin C-terminal domain | 197 | 304 | 0.000 |
| 7 | g5478.t3 | ProSiteProfiles | PS50268 | Cadherins domain profile. | 50 | 157 | 8.555 |
| 8 | g5478.t3 | ProSiteProfiles | PS50180 | Gamma-adaptin ear (GAE) domain profile. | 192 | 304 | 40.581 |
| 5 | g5478.t3 | SMART | SM00809 | alpha_adaptinc2 | 190 | 304 | 0.000 |
| 4 | g5478.t3 | SUPERFAMILY | SSF49348 | Clathrin adaptor appendage domain | 193 | 305 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5478/g5478.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5478.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016020 | membrane | CC |
| GO:0006886 | intracellular protein transport | BP |
| GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | BP |
| GO:0005509 | calcium ion binding | MF |
| GO:0016192 | vesicle-mediated transport | 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.
