General information for g987.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Carotenoid isomerooxygenase.
Parent gene
- The parent gene g987 is located on chr_3: 7267154..7269554 (+ 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_3 | g987 | g987.t2 | TSS | g987.t2 | 7266667 | 7266667 |
| chr_3 | g987 | g987.t2 | isoform | g987.t2 | 7266668 | 7269554 |
| chr_3 | g987 | g987.t2 | exon | g987.t2.exon1 | 7266668 | 7266814 |
| chr_3 | g987 | g987.t2 | cds | g987.t2.CDS1 | 7266719 | 7266814 |
| chr_3 | g987 | g987.t2 | exon | g987.t2.exon2 | 7267559 | 7268001 |
| chr_3 | g987 | g987.t2 | cds | g987.t2.CDS2 | 7267559 | 7268001 |
| chr_3 | g987 | g987.t2 | exon | g987.t2.exon3 | 7268197 | 7269115 |
| chr_3 | g987 | g987.t2 | cds | g987.t2.CDS3 | 7268197 | 7269115 |
| chr_3 | g987 | g987.t2 | exon | g987.t2.exon4 | 7269180 | 7269554 |
| chr_3 | g987 | g987.t2 | cds | g987.t2.CDS4 | 7269180 | 7269554 |
| chr_3 | g987 | g987.t2 | TTS | g987.t2 | 7269648 | 7269648 |
Sequences
>g987.t2 Gene=g987 Length=1884
AGTCTTTCATCTCATATCAAAATATCAACAGTGAAATATCAAAAAAATAAAATGTTTTCA
ATTTTCATTGACGAGGATGTTGATTTCCCTATTGAGCTTATTAGTGATATTTATAGTGAA
ATGCTGTCAATTAAAAACATTAGAAAGATTATCAACGATGAAGATGATGAAATTGAAATT
GTTGATTTGGATGAAGATGAAGATGAAGGAAATTTTAGTTTTAATCCTAAAACAAAATTG
AAAGAAAATTTATATCCAAATTGTGATGTGAATGTTTGGTTGAGATCATGCGAGCATGAA
ATTATTGAACCAATTCGTGGAGAAGTCAGTGGACAAATTCCAAAATGGATTAATGGAAGT
TTGTTAAGAAATGGACCAGGAAGCATAAAAGTTGGTTCAATGACTTTCAATCATCTTTTT
GATAGTTCAGCTTTGCTTCATAGATTTGATATTTTTCATGGAAATGTTACTTATCAGTGC
AGATTTTTGAAGAGTGACGCTTATAAAAAAAATTTAGCTGCTAATCGTGTTGTTGTGACT
GAGTTTGGTACTGCAAGCTGTCCTGATCCTTGCCAGAGTATTTTTCAAAGAGTTGCATCA
CTTTTTAAACCAGCTGACGCAAATTCAGATAACGCAATGATATCAATTTATCCATTTAAT
GATGAATATTTTTGTTTTGCTGAGAGTCCAATAATTCACAAAATTGATTCAGTAACACTT
GAGACACTTGAAAAATTAAATTTACATGAAAAATATGGAATAGTCAATCACACTTCGCAT
CCACATGTTATGAGTGATGGAACAGTTTACAATGTTGGATTAACTGTCACAAAATCAGGA
CCGGCTTATTGTGTTTTATGTTTTCCAAATGGTGAGAATATGTTTGATAATGCAAGGGTT
GTTGCAGAATTGCCAACACGTTGGAAACTTCATCCAAGTTACATGCATACTTTTGGAATT
ACTGAGCATTTTTTCATAATCGTTGAACAACCTTTGACAGTTTCTGTACCGGCAGTTGTT
AAATCACAATTGATGAATGAGCCTATGATTTCATGCCTTAAATGGTTTCCTGATAAATCG
ACAAACATTTACTTAATTGATCGTGAGAATGGTCAACTGCGACACACATTTCAAGCTGAA
GCATTTTTCTTTTTGCATATTATTAATCAATATGAAAAAGATGATCATGTTATACTCGAT
ATAAGTTGCTATAAAGATCCAGAAATGCTAAATTGCATGTATATTGATAGCATGAAAAAT
ATGCAAAATAATCCCGATTATGCCAAACTTTTCCGTGGTCGACCATTGAGATTTGTTTTG
CCATTAAAATACCCAACAAAATTGAAATCATTGACAAACTTTTTCGCATGGAATTATGAA
ACAAATGAAGAAAGTTTTAAAGTTATTGGAGAAAATTTGGTTAATCTCAAAGATAGTGAA
GCTACAGCATTTTCATTACCTGATGGATCAATTTTTTGCAAACCAGAACTTCTTTGCAAT
TTAGGATGTGAAACACCAAGGATTCATTACGAGCAACATTTGGGTGTTGAATATCAATAT
TTTTATGCAATTAGTTCTGATGTTGATGCATCTAATCCTGGAACGTTAATAAAAGTTGAT
GTTGTGAACAAAACAAAGCTGACATGGTGTGAGACAAATGTCTATCCAAGTGAACCAATA
TTTGTTCCTTCGCCTGATCCTCAAACTGAAGATGATGGTGTAATTTTGGCATCAATGGTT
TGGGGAAATGGTGATGAAAATCATGTTGGTTTACTTGTACTTGATGCTAAAAATATGCAA
GAACTTGGAAGATGTGAATTCAAAAATTTACCAGGACCTGTTCCAAAATGTCTTCATGGA
TGGTTTGCAGAGAGAAAATTTTAA
>g987.t2 Gene=g987 Length=610
MFSIFIDEDVDFPIELISDIYSEMLSIKNIRKIINDEDDEIEIVDLDEDEDEGNFSFNPK
TKLKENLYPNCDVNVWLRSCEHEIIEPIRGEVSGQIPKWINGSLLRNGPGSIKVGSMTFN
HLFDSSALLHRFDIFHGNVTYQCRFLKSDAYKKNLAANRVVVTEFGTASCPDPCQSIFQR
VASLFKPADANSDNAMISIYPFNDEYFCFAESPIIHKIDSVTLETLEKLNLHEKYGIVNH
TSHPHVMSDGTVYNVGLTVTKSGPAYCVLCFPNGENMFDNARVVAELPTRWKLHPSYMHT
FGITEHFFIIVEQPLTVSVPAVVKSQLMNEPMISCLKWFPDKSTNIYLIDRENGQLRHTF
QAEAFFFLHIINQYEKDDHVILDISCYKDPEMLNCMYIDSMKNMQNNPDYAKLFRGRPLR
FVLPLKYPTKLKSLTNFFAWNYETNEESFKVIGENLVNLKDSEATAFSLPDGSIFCKPEL
LCNLGCETPRIHYEQHLGVEYQYFYAISSDVDASNPGTLIKVDVVNKTKLTWCETNVYPS
EPIFVPSPDPQTEDDGVILASMVWGNGDENHVGLLVLDAKNMQELGRCEFKNLPGPVPKC
LHGWFAERKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g987.t2 | PANTHER | PTHR10543 | BETA-CAROTENE DIOXYGENASE | 68 | 607 | 0 |
| 3 | g987.t2 | PANTHER | PTHR10543:SF57 | RETINOID ISOMEROHYDROLASE | 68 | 607 | 0 |
| 1 | g987.t2 | Pfam | PF03055 | Retinal pigment epithelial membrane protein | 78 | 606 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K18048 (carotenoid isomerooxygenase)
Pathway
This gene does not belong to any 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.
