General information for g5595.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Carnitine O-palmitoyltransferase 2, mitochondrial.
Parent gene
- The parent gene g5595 is located on chr_2: 10448950..10452059 (- 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 | g5595 | g5595.t1 | TTS | g5595.t1 | 10446715 | 10446715 |
| chr_2 | g5595 | g5595.t1 | isoform | g5595.t1 | 10446909 | 10448950 |
| chr_2 | g5595 | g5595.t1 | exon | g5595.t1.exon1 | 10446909 | 10448608 |
| chr_2 | g5595 | g5595.t1 | cds | g5595.t1.CDS1 | 10446909 | 10448608 |
| chr_2 | g5595 | g5595.t1 | exon | g5595.t1.exon2 | 10448668 | 10448950 |
| chr_2 | g5595 | g5595.t1 | cds | g5595.t1.CDS2 | 10448668 | 10448950 |
| chr_2 | g5595 | g5595.t1 | TSS | g5595.t1 | 10448983 | 10448983 |
Sequences
>g5595.t1 Gene=g5595 Length=1983
ATGAAAGTGTTGAGTGCAAGTCATTTTCCTTCGGTTCGTCATCGAATCGATGTACAATAT
GCTAGTATCGTAAGATTTCTGTCACAAAACAGAAACGATGATGGATATCAATATTTACAC
AAATCAAATATGCCAACATACTATTTCCAAAAGTCACTGCCTCGACTCCCTATTCCAAAA
ATTGAAAAAACCCTTTCAAGATATTTAGACGCCCAACGACCCTTGCTTTCTGATGAAGAA
TTTAAAAAAACACAAGATGCATGCAACAAATTTGTTAAATCAGGTGGTTGGGAACTTCAA
GCAATGTTGAAAGAGAAGGATAAAGTGAATAAGCACACATCATATATCTCTGAGCCTTGG
TACACAATGTATTTGAAGGATCGTGCACCATTGCCTGTCAATTATAATCCTGTATTAATA
ATGAAGCATGACACTAGACCTGAATACAATGATCAAGCTATTCGAACGGCAAATGTCATT
ATTAGTTCAATGCGATTTATGCGTTCCCTTAATGAAGAAGTGCTTGTACCAGAAATATAT
CATATGGATCCATCTAAAACAGACACTGAAGCATTTAGAGCAAAAATCATGCGTTTTCCA
TCATTTATAGCCACATATGCTGCCTATTACTATAAAGCTTATCCCCTAGATATGGTACAA
TTTCAGGGACTTTTTGCAGCTACTAGAATTCCTAAAAGAGATAAAGATGAAATTGTTAGA
TTCAAGGATGTGAGACATGTGTTAGTAACAAGAAATGGTCACTTTTATTATGTTGAAGTG
CTTGATTCTGATGGCAATATTCGTGATCCAGAATTCATTTATTCACAAATTAAATATTTA
TTGACAATAAGTGAAGATCAAAATTCACATCCAATTGGTGCATTGACAACACAAAATAGA
AGAATTTGGTGGAATGCGAGAGAGCATTTGATTTCATCGAGTGCGAAGAATGCTGACAAC
TTGAAAGCAATCGATTCAGCTCTGTTCTGTATTAATCTAGATGAAACCAAATATAACGAA
GAAAATCCCGTTCCAGCTGTTAGAGATTTTCTTTTTGATTCTTGTAAAAATCGTTGGTAT
GACAAATCATTGAGTGTGATAATTGATAAATCAGGAACCACTGGCGTCACATTTGAGCAT
TCGCCAACTGATGGTGTTTCTGTTTTGCGTTATTTTAATGAAATTTATAAAGACATGAAC
AAATCATTTGTAGGACCTGAGACTAAACTTGTAAAAGGTGTTGAAACAACTGTCAGAAAG
CTTGACTTTGACATTGATGATAAATCAAAAAATGATATTGAAACAGCAATAAGTGCTCAT
CAAAATGTAGTTGGATCAATTGATATGAACTTCCTTAAGTATCAAAAACTTAACAAAGTT
GAATGTAAAAAGTACAAAATCAGTCCCGATTCAATTATGCAGTTAGGCTTTCAACTTGCT
TATTACAGACAAAACAAGAAATTTGTTGCAACATATGAAAGCTGCTCAACTTCCGCATTC
CGTCACGGCCGGACAGAAACGATGAGACCATGTACAATTGAAACAAAAGCATTTGTAGAA
GCAATTGATGGTAAAAACAAACCGTCAAATAAACAATTACGTGCAATGCTGGATCAATGT
TCAAAGAAACATAATCAGTTAACAAAAGATGCCGCAATGGGACAAGGTTTTGACCGACAT
TTATTTGCATTAAGAACAGCAGCAGAGAGAGTGAGAATAGTTGATGACTTTGATATTTTT
AAAGATCCAGCATATAAAAGAATCAATCATTATATTTTATCAACAAGCACTTTGACGAGC
AATGGTTTACTTGCGGGAGGTTTTGGACCAGTTGTAAAAGACGGTTATGGAATTGGTTAT
AATATTCAAGAAGAATTGCTTGGTTGTGTAGTTAGTAATTATAAAAATGAAACAAATAGT
AAAGAATTTCTCGAATGTTTAAAGAGTGCATACGATGATTTAACTGACGTTATCAAAGCT
TAA
>g5595.t1 Gene=g5595 Length=660
MKVLSASHFPSVRHRIDVQYASIVRFLSQNRNDDGYQYLHKSNMPTYYFQKSLPRLPIPK
IEKTLSRYLDAQRPLLSDEEFKKTQDACNKFVKSGGWELQAMLKEKDKVNKHTSYISEPW
YTMYLKDRAPLPVNYNPVLIMKHDTRPEYNDQAIRTANVIISSMRFMRSLNEEVLVPEIY
HMDPSKTDTEAFRAKIMRFPSFIATYAAYYYKAYPLDMVQFQGLFAATRIPKRDKDEIVR
FKDVRHVLVTRNGHFYYVEVLDSDGNIRDPEFIYSQIKYLLTISEDQNSHPIGALTTQNR
RIWWNAREHLISSSAKNADNLKAIDSALFCINLDETKYNEENPVPAVRDFLFDSCKNRWY
DKSLSVIIDKSGTTGVTFEHSPTDGVSVLRYFNEIYKDMNKSFVGPETKLVKGVETTVRK
LDFDIDDKSKNDIETAISAHQNVVGSIDMNFLKYQKLNKVECKKYKISPDSIMQLGFQLA
YYRQNKKFVATYESCSTSAFRHGRTETMRPCTIETKAFVEAIDGKNKPSNKQLRAMLDQC
SKKHNQLTKDAAMGQGFDRHLFALRTAAERVRIVDDFDIFKDPAYKRINHYILSTSTLTS
NGLLAGGFGPVVKDGYGIGYNIQEELLGCVVSNYKNETNSKEFLECLKSAYDDLTDVIKA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5595.t1 | Coils | Coil | Coil | 530 | 550 | - |
| 7 | g5595.t1 | Gene3D | G3DSA:1.20.1280.180 | - | 48 | 215 | 8.3E-236 |
| 9 | g5595.t1 | Gene3D | G3DSA:3.30.559.40 | - | 55 | 651 | 8.3E-236 |
| 8 | g5595.t1 | Gene3D | G3DSA:3.30.559.70 | - | 135 | 610 | 8.3E-236 |
| 2 | g5595.t1 | PANTHER | PTHR22589 | CARNITINE O-ACYLTRANSFERASE | 28 | 659 | 3.1E-239 |
| 3 | g5595.t1 | PANTHER | PTHR22589:SF16 | CARNITINE O-PALMITOYLTRANSFERASE 2, MITOCHONDRIAL | 28 | 659 | 3.1E-239 |
| 1 | g5595.t1 | Pfam | PF00755 | Choline/Carnitine o-acyltransferase | 53 | 654 | 4.1E-187 |
| 6 | g5595.t1 | ProSitePatterns | PS00440 | Acyltransferases ChoActase / COT / CPT family signature 2. | 358 | 385 | - |
| 5 | g5595.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 45 | 443 | 7.23E-111 |
| 4 | g5595.t1 | SUPERFAMILY | SSF52777 | CoA-dependent acyltransferases | 447 | 659 | 7.23E-69 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5595/g5595.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5595.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016746 | acyltransferase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08766 (carnitine O-palmitoyltransferase 2)
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.
