General information for g4999.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative CD63 antigen.
Parent gene
- The parent gene g4999 is located on chr_2: 6381563..6384105 (- 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 | g4999 | g4999.t1 | TTS | g4999.t1 | 6381197 | 6381197 |
| chr_2 | g4999 | g4999.t1 | isoform | g4999.t1 | 6381563 | 6383219 |
| chr_2 | g4999 | g4999.t1 | exon | g4999.t1.exon1 | 6381563 | 6381836 |
| chr_2 | g4999 | g4999.t1 | cds | g4999.t1.CDS1 | 6381563 | 6381836 |
| chr_2 | g4999 | g4999.t1 | exon | g4999.t1.exon2 | 6382237 | 6382604 |
| chr_2 | g4999 | g4999.t1 | cds | g4999.t1.CDS2 | 6382237 | 6382604 |
| chr_2 | g4999 | g4999.t1 | exon | g4999.t1.exon3 | 6383154 | 6383219 |
| chr_2 | g4999 | g4999.t1 | cds | g4999.t1.CDS3 | 6383154 | 6383219 |
| chr_2 | g4999 | g4999.t1 | TSS | g4999.t1 | 6384096 | 6384096 |
Sequences
>g4999.t1 Gene=g4999 Length=708
ATGGCAAAGGGATTTGGCATCAACTGCATTAAGTATCTAGTCTTCTTTTTCAACTTTTTG
TTCGCTATGACAGGACTATTAACAATTATAGTCGGCGCGATTATTCAGAGTTCATATCAT
CATTATGAAAACTTTATTGGAGAATCTTTTTGGAGCGCTCCGATTATTCTTATGATAGTG
GGTTCATTAATCTTCTTCATATCATTCCTGGGATGCTGTGGAGCATTACGAGAATCGTCT
TGTTTGATATTGACATTTTCAGTCTTCTTGCTATTTGTGTTTATCACTGAAATTGGCATT
GGTGTTGCTGGCTATATCAAACATGCTGAATTACCTGGTATTCTTGAGCGTCAATTCAAT
AGAACTTTGGATGACTACACAACATCAATTGAGGCTCAACAGGCATGGAGTTTGGTTCAA
GGTGAATTGCAATGCTGCGGAATTTATGGACCGTTAGACTGGAAACCAATTTTCAAAAAC
AAAACTGTACCATCCACATGTTGTCACATTCTTCCAGTGAACGTGAAAAATTGTGAAGTC
AAATATTCATCTGAAGAAGGTTGCTATCAAAAGCTTTTGGATTTCCTTGATACAAAATCG
TTGTTATTGGGAGGTGTTGGTGTTGGAATAGCCATAATTCAACTTCTTGGTGTCATTTTT
GCATGTGCACTGTCACGAGCATTCCGTGAAAATTATGAGACAGTTTAA
>g4999.t1 Gene=g4999 Length=235
MAKGFGINCIKYLVFFFNFLFAMTGLLTIIVGAIIQSSYHHYENFIGESFWSAPIILMIV
GSLIFFISFLGCCGALRESSCLILTFSVFLLFVFITEIGIGVAGYIKHAELPGILERQFN
RTLDDYTTSIEAQQAWSLVQGELQCCGIYGPLDWKPIFKNKTVPSTCCHILPVNVKNCEV
KYSSEEGCYQKLLDFLDTKSLLLGGVGVGIAIIQLLGVIFACALSRAFRENYETV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g4999.t1 | CDD | cd03127 | tetraspanin_LEL | 105 | 199 | 6.57369E-18 |
| 9 | g4999.t1 | Gene3D | G3DSA:1.10.1450.10 | Tetraspanin | 110 | 198 | 2.9E-10 |
| 2 | g4999.t1 | PANTHER | PTHR19282:SF273 | TETRASPANIN | 6 | 231 | 4.9E-49 |
| 3 | g4999.t1 | PANTHER | PTHR19282 | TETRASPANIN | 6 | 231 | 4.9E-49 |
| 19 | g4999.t1 | PIRSF | PIRSF002419 | Tetraspanin | 1 | 234 | 2.7E-49 |
| 7 | g4999.t1 | PRINTS | PR00259 | Transmembrane four family signature | 12 | 35 | 8.0E-41 |
| 4 | g4999.t1 | PRINTS | PR00259 | Transmembrane four family signature | 50 | 76 | 8.0E-41 |
| 6 | g4999.t1 | PRINTS | PR00259 | Transmembrane four family signature | 77 | 105 | 8.0E-41 |
| 5 | g4999.t1 | PRINTS | PR00259 | Transmembrane four family signature | 202 | 228 | 8.0E-41 |
| 1 | g4999.t1 | Pfam | PF00335 | Tetraspanin family | 10 | 226 | 5.9E-52 |
| 10 | g4999.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 18 | g4999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 35 | - |
| 13 | g4999.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 36 | 54 | - |
| 17 | g4999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 76 | - |
| 12 | g4999.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 77 | 82 | - |
| 15 | g4999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 83 | 106 | - |
| 14 | g4999.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 107 | 200 | - |
| 16 | g4999.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 201 | 224 | - |
| 11 | g4999.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 225 | 235 | - |
| 25 | g4999.t1 | ProSitePatterns | PS00421 | Transmembrane 4 family signature. | 61 | 83 | - |
| 8 | g4999.t1 | SUPERFAMILY | SSF48652 | Tetraspanin | 106 | 199 | 7.72E-15 |
| 22 | g4999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 21 | g4999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 50 | 72 | - |
| 23 | g4999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 106 | - |
| 24 | g4999.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 224 | - |
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:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K06497 (CD63 antigen)
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.
