General information for g9966.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein peste.
Parent gene
- The parent gene g9966 is located on chr_1: 6289710..6290898 (+ 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_1 | g9966 | g9966.t1 | TSS | g9966.t1 | 6287168 | 6287168 |
| chr_1 | g9966 | g9966.t1 | isoform | g9966.t1 | 6287635 | 6289710 |
| chr_1 | g9966 | g9966.t1 | exon | g9966.t1.exon1 | 6287635 | 6287772 |
| chr_1 | g9966 | g9966.t1 | cds | g9966.t1.CDS1 | 6287635 | 6287772 |
| chr_1 | g9966 | g9966.t1 | exon | g9966.t1.exon2 | 6288367 | 6289710 |
| chr_1 | g9966 | g9966.t1 | cds | g9966.t1.CDS2 | 6288367 | 6289710 |
| chr_1 | g9966 | g9966.t1 | TTS | g9966.t1 | 6289799 | 6289799 |
Sequences
>g9966.t1 Gene=g9966 Length=1482
ATGGAACAGAAAAATTCAAAAATATCAGGATCAAAGTCTTGGTGTTGTAAATATAATATA
ATTGCAGTTACTTTGATAGCATTTGGAATTTCTATGCTTCTTTTTCTTCCCGATTATCTT
CAAAAACAAATGAATATCAATCTTGAACTTCAACCCGATTCACGAACTTTTCCAGAATGG
AAAAAGCCAACAGTTCCACTTTACATGGATATTTACATTTTTAACTGGACAAATCCAGAA
GATATCAATAATCACACAACAAAGCCTATTGTGAAACAGCTTGGCCCTTATCGATTTAGA
GAATATCCCGATAAACACAATATTACTTTCCATGATAATAATAATACAGTAACTTATCGA
AAATCATCATTATTTTATTTCGAAGAAAATGGTAGTAATGGGACTTTAGATGATGTTGTA
TCAGTTGTTAATATGCTTGCTGTAGGTGCAGCAGCTACTGCTCAATATTGGGGATTTTTA
AGACAATTAAGTGTCTCTACATCATTGAGCGGATTTGGTCAGAAAATTAGTGTCAGAAAG
ACAGTTCGTGAAATTCTTTTTGAAGGTTATTACGACTCTATGCTAACGATCGGTTCAATG
TTTGATTCAGAAGCTACACTATTTGATACAGTTGGTTTTATGGTTAAGAAAAATGGAACA
GATCTGTTAACAGGAAAATATAATGTGCACACAGGAGTTGGTGATATTTCAAAGCTTGGA
CAAATTCAAAAATATCGTGATCTTAATGAGTTTCCTTATTATGAAGGAGAATGTAGAAAA
CTAAAAGGCAGTCCAGGAGAATTTTATCCTCCCGGAAGATCATCGAATGATATTCTTTAT
CTTTTTACTCCTGAATTATGTAGAGCATTGCCATATGAATATAAGAAAGATATAAATCAT
CTTGGTATAAAAGGAAATCGCTATTATTTGGATGATCGTGCAATTGATAATGGTGAAAAA
TACTCAGAAAATAGTTGTTACATGACTGAGTCTCTTCCTTCTGGTTTCATCAACATTTCA
GCATGTAATTTTGGTCAACCTCTATATATGTCGTATCCTCATTTTTATAAAGCTGATAAG
AGTTTCTTAGATGCAATTGATGGATTGTCTCCACAAAAAGATCTTCACGAGTCTTACATC
ACACTTGAGCCTAAAACTTCAGTAACGCTTGAAGCTGTTGGAAGACTACAAACAAATCTT
TATCTCCGTCCATATGGTTTCATAAATTTATTCAAAAATGTTCCCAGATTGATGCTGCCA
TTATTTTTTGTAGAACAAAAATTCATAATGGGAGAAGAACATGCGAGTGAACTTTATTAT
GGTCTGCTTATATTTAGTGTATCAAAATATATTGGAGTTTTACTCATTATTGTTGGTGTT
GCATTTATTGCATGTCGTCGATGTATGCAATGTAAATCAAAACAAGATAATAAGAATGAC
TTAGAAATTAATGAAAAAGAAGCAACTGCTTTGATGACGTAA
>g9966.t1 Gene=g9966 Length=493
MEQKNSKISGSKSWCCKYNIIAVTLIAFGISMLLFLPDYLQKQMNINLELQPDSRTFPEW
KKPTVPLYMDIYIFNWTNPEDINNHTTKPIVKQLGPYRFREYPDKHNITFHDNNNTVTYR
KSSLFYFEENGSNGTLDDVVSVVNMLAVGAAATAQYWGFLRQLSVSTSLSGFGQKISVRK
TVREILFEGYYDSMLTIGSMFDSEATLFDTVGFMVKKNGTDLLTGKYNVHTGVGDISKLG
QIQKYRDLNEFPYYEGECRKLKGSPGEFYPPGRSSNDILYLFTPELCRALPYEYKKDINH
LGIKGNRYYLDDRAIDNGEKYSENSCYMTESLPSGFINISACNFGQPLYMSYPHFYKADK
SFLDAIDGLSPQKDLHESYITLEPKTSVTLEAVGRLQTNLYLRPYGFINLFKNVPRLMLP
LFFVEQKFIMGEEHASELYYGLLIFSVSKYIGVLLIIVGVAFIACRRCMQCKSKQDNKND
LEINEKEATALMT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g9966.t1 | PANTHER | PTHR11923 | SCAVENGER RECEPTOR CLASS B TYPE-1 SR-B1 | 15 | 480 | 6.7E-147 |
| 3 | g9966.t1 | PANTHER | PTHR11923:SF93 | GH07959P-RELATED | 15 | 480 | 6.7E-147 |
| 4 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 62 | 83 | 7.4E-40 |
| 7 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 88 | 100 | 7.4E-40 |
| 5 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 116 | 135 | 7.4E-40 |
| 9 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 258 | 282 | 7.4E-40 |
| 6 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 331 | 355 | 7.4E-40 |
| 8 | g9966.t1 | PRINTS | PR01609 | Adhesion molecule CD36 family signature | 378 | 399 | 7.4E-40 |
| 1 | g9966.t1 | Pfam | PF01130 | CD36 family | 20 | 465 | 3.6E-141 |
| 12 | g9966.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 19 | - |
| 16 | g9966.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 40 | - |
| 14 | g9966.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 41 | 437 | - |
| 15 | g9966.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 438 | 465 | - |
| 13 | g9966.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 466 | 493 | - |
| 11 | g9966.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 10 | g9966.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 442 | 464 | - |
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:0016020 | membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K12384 (lysosome membrane protein 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.
