General information for g5166.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Microsomal triglyceride transfer protein large subunit.
Parent gene
- The parent gene g5166 is located on chr_2: 7404054..7406339 (- 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 | g5166 | g5166.t4 | TTS | g5166.t4 | 7403012 | 7403012 |
| chr_2 | g5166 | g5166.t4 | isoform | g5166.t4 | 7404054 | 7406339 |
| chr_2 | g5166 | g5166.t4 | exon | g5166.t4.exon1 | 7404054 | 7405525 |
| chr_2 | g5166 | g5166.t4 | cds | g5166.t4.CDS1 | 7404056 | 7405525 |
| chr_2 | g5166 | g5166.t4 | exon | g5166.t4.exon2 | 7405618 | 7405793 |
| chr_2 | g5166 | g5166.t4 | cds | g5166.t4.CDS2 | 7405618 | 7405793 |
| chr_2 | g5166 | g5166.t4 | exon | g5166.t4.exon3 | 7406285 | 7406339 |
| chr_2 | g5166 | g5166.t4 | cds | g5166.t4.CDS3 | 7406285 | 7406339 |
| chr_2 | g5166 | g5166.t4 | TSS | g5166.t4 | 7406490 | 7406490 |
Sequences
>g5166.t4 Gene=g5166 Length=1703
ATGGCATTTGAGTGTATTTGTAGAAAAATATTAATTTTTATGTGCCTCTTAACCGTGAGC
ATTCACGCGTTTGAATTAGGAACAGAAAGAACATTTTCATTCGTTAATGATGTTAATTTG
TATGAATTGAAACTATCAACAAGTCAGGCAATTGGCTATCGAACGTCCGGTGAAATAAAG
GTCTCAACTATCTATGAAGATAATGAACATGGATTTTTATTACGATTCGAGCTTCTATCG
CCGCAATTGTATATGGAAAAGTTTAAAGTTCAACCAATGGACTATGATGAAAAGTCATCG
ATTCTTGATAAATATAAGAAATCCATCTTTTACGCTTATTGGAAAGCAGGAATTATCGAA
AAATCATTTATTAAAAATACCAAAGATTCATCGTTGAATAACTTTTTAAGGTCAATATTG
AGTCTCTTTCAATATCAACTTTTGGATACAAAAACAACTGAAAAAGATATTTCAGGAACG
TGTCAGGTTAAATATGTGGCAAAATCTTCAACCAAATTTCTAAAAATCAAGTCTGATTGC
ACTGCTATAGAGCAACATGAACGATTAGATCAACCGTTAGGGAATGAAGTAAAACTTACG
CGTGTAACAGTTATTGAAACTTCAACATTAGGAGAAATTGAAACTCTTCACAGTTCTGAT
CATCATCAGTTCTATATCAATGCTTATAAACATGTCGGTTACAAAGTTGGCTCAATCTTT
TATTTAAAATCTGATGGAACGATAAAAGATTGTGAAGTGATAAAAGCTGATAATTTAGAA
AATGCTATCAAGACATTAGAAGGATTTATTGAAACTTCTATACTGCCTGAAATTAATTTT
GATAAGTCTACAGATGTGACAATAGTTAAACAATTGAAGGAATTGAAAGAGAATCTTAGT
AATGAAAAAGTTGGTAAGGAGACATCAGCTTTAGCTCTTTTAAAACTTTTGCAAACTGGA
AGACAATCGAAAGCTGAAGATTTAATAAGAATTGTTAATGCAAGAACAACTAAAGAGATT
AAAGGACAGATAATGGATCTTTTAGCAGCAATTCAAACAGAAGAGTCACATGAAGCATTT
AGAAGCACAATGAATTTTACAAACGAAGAAGAGTTTGATAATATTGAGAGATATTTGCAG
TCATTATCAGTTGGTGTTTTACCTCGTGAGTCAGTCATTAAAAACATCTTTGAAGTACTG
ATTAATGATAATATTCAAAATGAAAAACTCAAAGACACGCTCGTGCAGACTATTGCATCA
ATGTGTAAAAAATTCACTAATCTTCCAAACCAGAGTTATGACAGTGAAATTGTTGTCAAG
TTCAAAAACTTTTTACTTGAGTCTATCGATAGCTGTACTAATAATGATTGCAAAGAAATT
TACATACGTGGCCTTCAAAATCTTCAATCGCCAAATATTATTGATAAATTAGTCATGCTG
GCACTAAATGAGCCATATCAAATTTCAGTAGCAGCAATGAAAGCACTCAATCAATTTCCA
TCAACAATTTTGCAAGGTGACAAGAAGCAATTTGAGAGCATTTTTTACCAACAAAAGAAA
AAGTTTGATACAAGTGCACGAACAATTGCTTTAGATATTTTATTAAGACTTAAACCGGAA
ACAAAAGATATCATGAATTTTGTTTCATATTTAAAATCAAATGATCCGGCATATGAAGTC
AAACAATATTTAGTACAAAAATT
>g5166.t4 Gene=g5166 Length=567
MAFECICRKILIFMCLLTVSIHAFELGTERTFSFVNDVNLYELKLSTSQAIGYRTSGEIK
VSTIYEDNEHGFLLRFELLSPQLYMEKFKVQPMDYDEKSSILDKYKKSIFYAYWKAGIIE
KSFIKNTKDSSLNNFLRSILSLFQYQLLDTKTTEKDISGTCQVKYVAKSSTKFLKIKSDC
TAIEQHERLDQPLGNEVKLTRVTVIETSTLGEIETLHSSDHHQFYINAYKHVGYKVGSIF
YLKSDGTIKDCEVIKADNLENAIKTLEGFIETSILPEINFDKSTDVTIVKQLKELKENLS
NEKVGKETSALALLKLLQTGRQSKAEDLIRIVNARTTKEIKGQIMDLLAAIQTEESHEAF
RSTMNFTNEEEFDNIERYLQSLSVGVLPRESVIKNIFEVLINDNIQNEKLKDTLVQTIAS
MCKKFTNLPNQSYDSEIVVKFKNFLLESIDSCTNNDCKEIYIRGLQNLQSPNIIDKLVML
ALNEPYQISVAAMKALNQFPSTILQGDKKQFESIFYQQKKKFDTSARTIALDILLRLKPE
TKDIMNFVSYLKSNDPAYEVKQYLVQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5166.t4 | Coils | Coil | Coil | 289 | 309 | - |
| 5 | g5166.t4 | Gene3D | G3DSA:2.30.230.10 | - | 27 | 231 | 2.7E-7 |
| 1 | g5166.t4 | PANTHER | PTHR13024 | MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN, LARGE SUBUNIT | 13 | 567 | 1.4E-98 |
| 8 | g5166.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 9 | g5166.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 10 | g5166.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 18 | - |
| 11 | g5166.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 7 | g5166.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 567 | - |
| 13 | g5166.t4 | ProSiteProfiles | PS51211 | Vitellogenin domain profile. | 24 | 567 | 10.199 |
| 12 | g5166.t4 | SMART | SM00638 | lpd_n | 24 | 567 | 1.0E-4 |
| 3 | g5166.t4 | SUPERFAMILY | SSF56968 | Lipovitellin-phosvitin complex; beta-sheet shell regions | 46 | 171 | 2.12E-9 |
| 2 | g5166.t4 | SUPERFAMILY | SSF48431 | Lipovitellin-phosvitin complex, superhelical domain | 281 | 561 | 4.32E-15 |
| 4 | g5166.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5166/g5166.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5166.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005319 | lipid transporter activity | MF |
| GO:0006869 | lipid transport | BP |
| GO:0005548 | phospholipid transporter activity | 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. There were no conditions that were differentially expressed