General information for g5166.t3
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.t3 | isoform | g5166.t3 | 7404054 | 7406339 |
| chr_2 | g5166 | g5166.t3 | exon | g5166.t3.exon1 | 7404054 | 7405525 |
| chr_2 | g5166 | g5166.t3 | cds | g5166.t3.CDS1 | 7404056 | 7405504 |
| chr_2 | g5166 | g5166.t3 | exon | g5166.t3.exon2 | 7405618 | 7406339 |
| chr_2 | g5166 | g5166.t3 | TTS | g5166.t3 | 7405985 | 7405985 |
| chr_2 | g5166 | g5166.t3 | TSS | g5166.t3 | 7406490 | 7406490 |
Sequences
>g5166.t3 Gene=g5166 Length=2194
ATGGCATTTGAGTGTATTTGTAGAAAAATATTAATTTTTATGTGCCTCTTAACCGGTAAG
TGAAGATCGTCAAGATTAAAATATTTTACTCTGTATTCGAATGCTATTATCACAAGGGCA
ATAAGAATTTTAAATGATAACATTGCTGACCTCACTTAGAAATGTCGCTGACTCAATAGA
AATCTCTCGATGCAAAATAAAAATAAAAAAGGTTTAAACTTGAAAGAAATTATTAATTAC
GTGGACATTGATGAAATGTGAGAACATGAGAGAGAGAGAGAGAGTCAAAGAAGAAGCAGA
GAACAGATTTGTTGTCTGGAATTCTAAAAATAATCTTTAGTAGACATACAATATGAAAAA
AAGAGAGAAAAAAAGAGAATCTTGAAAAAAATAAGAGTCAATGCCCACATCTCGCTGTTT
TTCGTCAGCTGTTTATCCAAAATAAAAACGCGAGATTCACGCATGTTGAAAAGTGGTTTT
TACAACCGGTTTATTTATTGTTTTCTTTCTGATGCATAATATTCATTTCGTAATTAAATA
TTTCAGTGAGCATTCACGCGTTTGAATTAGGAACAGAAAGAACATTTTCATTCGTTAATG
ATGTTAATTTGTATGAATTGAAACTATCAACAAGTCAGGCAATTGGCTATCGAACGTCCG
GTGAAATAAAGGTCTCAACTATCTATGAAGATAATGAACATGGATTTTTATTACGATTCG
AGCTTCTATCGCCGCAATTGTATATGGAAAAGTTTAAAGTTCAACCAATGGACTATGATG
AAAAGTCATCGATTCTTGATAAATATAAGAAATCCATCTTTTACGCTTATTGGAAAGCAG
GAATTATCGAAAAATCATTTATTAAAAATACCAAAGATTCATCGTTGAATAACTTTTTAA
GGTCAATATTGAGTCTCTTTCAATATCAACTTTTGGATACAAAAACAACTGAAAAAGATA
TTTCAGGAACGTGTCAGGTTAAATATGTGGCAAAATCTTCAACCAAATTTCTAAAAATCA
AGTCTGATTGCACTGCTATAGAGCAACATGAACGATTAGATCAACCGTTAGGGAATGAAG
TAAAACTTACGCGTGTAACAGTTATTGAAACTTCAACATTAGGAGAAATTGAAACTCTTC
ACAGTTCTGATCATCATCAGTTCTATATCAATGCTTATAAACATGTCGGTTACAAAGTTG
GCTCAATCTTTTATTTAAAATCTGATGGAACGATAAAAGATTGTGAAGTGATAAAAGCTG
ATAATTTAGAAAATGCTATCAAGACATTAGAAGGATTTATTGAAACTTCTATACTGCCTG
AAATTAATTTTGATAAGTCTACAGATGTGACAATAGTTAAACAATTGAAGGAATTGAAAG
AGAATCTTAGTAATGAAAAAGTTGGTAAGGAGACATCAGCTTTAGCTCTTTTAAAACTTT
TGCAAACTGGAAGACAATCGAAAGCTGAAGATTTAATAAGAATTGTTAATGCAAGAACAA
CTAAAGAGATTAAAGGACAGATAATGGATCTTTTAGCAGCAATTCAAACAGAAGAGTCAC
ATGAAGCATTTAGAAGCACAATGAATTTTACAAACGAAGAAGAGTTTGATAATATTGAGA
GATATTTGCAGTCATTATCAGTTGGTGTTTTACCTCGTGAGTCAGTCATTAAAAACATCT
TTGAAGTACTGATTAATGATAATATTCAAAATGAAAAACTCAAAGACACGCTCGTGCAGA
CTATTGCATCAATGTGTAAAAAATTCACTAATCTTCCAAACCAGAGTTATGACAGTGAAA
TTGTTGTCAAGTTCAAAAACTTTTTACTTGAGTCTATCGATAGCTGTACTAATAATGATT
GCAAAGAAATTTACATACGTGGCCTTCAAAATCTTCAATCGCCAAATATTATTGATAAAT
TAGTCATGCTGGCACTAAATGAGCCATATCAAATTTCAGTAGCAGCAATGAAAGCACTCA
ATCAATTTCCATCAACAATTTTGCAAGGTGACAAGAAGCAATTTGAGAGCATTTTTTACC
AACAAAAGAAAAAGTTTGATACAAGTGCACGAACAATTGCTTTAGATATTTTATTAAGAC
TTAAACCGGAAACAAAAGATATCATGAATTTTGTTTCATATTTAAAATCAAATGATCCGG
CATATGAAGTCAAACAATATTTAGTACAAAAATT
>g5166.t3 Gene=g5166 Length=483
MEKFKVQPMDYDEKSSILDKYKKSIFYAYWKAGIIEKSFIKNTKDSSLNNFLRSILSLFQ
YQLLDTKTTEKDISGTCQVKYVAKSSTKFLKIKSDCTAIEQHERLDQPLGNEVKLTRVTV
IETSTLGEIETLHSSDHHQFYINAYKHVGYKVGSIFYLKSDGTIKDCEVIKADNLENAIK
TLEGFIETSILPEINFDKSTDVTIVKQLKELKENLSNEKVGKETSALALLKLLQTGRQSK
AEDLIRIVNARTTKEIKGQIMDLLAAIQTEESHEAFRSTMNFTNEEEFDNIERYLQSLSV
GVLPRESVIKNIFEVLINDNIQNEKLKDTLVQTIASMCKKFTNLPNQSYDSEIVVKFKNF
LLESIDSCTNNDCKEIYIRGLQNLQSPNIIDKLVMLALNEPYQISVAAMKALNQFPSTIL
QGDKKQFESIFYQQKKKFDTSARTIALDILLRLKPETKDIMNFVSYLKSNDPAYEVKQYL
VQK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5166.t3 | Coils | Coil | Coil | 205 | 225 | - |
| 5 | g5166.t3 | Gene3D | G3DSA:2.30.230.10 | - | 3 | 148 | 9.2E-7 |
| 1 | g5166.t3 | PANTHER | PTHR13024 | MICROSOMAL TRIGLYCERIDE TRANSFER PROTEIN, LARGE SUBUNIT | 17 | 483 | 2.7E-91 |
| 7 | g5166.t3 | ProSiteProfiles | PS51211 | Vitellogenin domain profile. | 1 | 483 | 9.449 |
| 4 | g5166.t3 | SMART | SM00638 | lpd_n | 2 | 483 | 0.0036 |
| 3 | g5166.t3 | SUPERFAMILY | SSF56968 | Lipovitellin-phosvitin complex; beta-sheet shell regions | 26 | 87 | 8.63E-9 |
| 2 | g5166.t3 | SUPERFAMILY | SSF48431 | Lipovitellin-phosvitin complex, superhelical domain | 197 | 477 | 2.75E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5166/g5166.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5166.t3.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.
