General information for g4999.t3
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.t3 | isoform | g4999.t3 | 6380047 | 6382604 |
| chr_2 | g4999 | g4999.t3 | exon | g4999.t3.exon1 | 6380047 | 6381836 |
| chr_2 | g4999 | g4999.t3 | cds | g4999.t3.CDS1 | 6381563 | 6381836 |
| chr_2 | g4999 | g4999.t3 | exon | g4999.t3.exon2 | 6382237 | 6382604 |
| chr_2 | g4999 | g4999.t3 | cds | g4999.t3.CDS2 | 6382237 | 6382604 |
| chr_2 | g4999 | g4999.t3 | TSS | g4999.t3 | NA | NA |
| chr_2 | g4999 | g4999.t3 | TTS | g4999.t3 | NA | NA |
Sequences
>g4999.t3 Gene=g4999 Length=2158
ATGACAGGACTATTAACAATTATAGTCGGCGCGATTATTCAGAGTTCATATCATCATTAT
GAAAACTTTATTGGAGAATCTTTTTGGAGCGCTCCGATTATTCTTATGATAGTGGGTTCA
TTAATCTTCTTCATATCATTCCTGGGATGCTGTGGAGCATTACGAGAATCGTCTTGTTTG
ATATTGACATTTTCAGTCTTCTTGCTATTTGTGTTTATCACTGAAATTGGCATTGGTGTT
GCTGGCTATATCAAACATGCTGAATTACCTGGTATTCTTGAGCGTCAATTCAATAGAACT
TTGGATGACTACACAACATCAATTGAGGCTCAACAGGCATGGAGTTTGGTTCAAGGTGAA
TTGCAATGCTGCGGAATTTATGGACCGTTAGACTGGAAACCAATTTTCAAAAACAAAACT
GTACCATCCACATGTTGTCACATTCTTCCAGTGAACGTGAAAAATTGTGAAGTCAAATAT
TCATCTGAAGAAGGTTGCTATCAAAAGCTTTTGGATTTCCTTGATACAAAATCGTTGTTA
TTGGGAGGTGTTGGTGTTGGAATAGCCATAATTCAACTTCTTGGTGTCATTTTTGCATGT
GCACTGTCACGAGCATTCCGTGAAAATTATGAGACAGTTTAAATGCATTTATTTTTTTAT
TACACGTACATGAGCCATGATCATCAAAATTATTATTACTAGTAGATTTAATATTGTCAT
AAAGCAACAGCATTAGAGCTTACAAAGAAAACATTCCTGACAATCTCATCGCGGATTGAA
TTAGAAAATTTATCGAGTCATATTATGTTGCTGAGGCTATTATATCATTAAAATTCTTTT
GAATCTCTTTCCTATAGTATTCAGTAGCAATGTGTTGAAGTAGTGATATTAAAAACAATA
TAAAAGGAAGAAAATGCTGATTGACTTGACTTTATGTTAGAATTTAAAAAAGTTCGTTTG
AATTTATTAGAGAGTGCAAAGCAAAAAAAAAGTTCAAAAGAAATTTAAAGCCAAAATAAA
AAAGACATAGATGGTAAAATCAGTGGGGATAAAATTAGCGAGAGAGTTCCTTCATATCAA
AAACAATATTTTTTAATGCAAAAATGCTCTTTACGAGTCTGAAGTCTTTTCTCAGCATCT
TTTGATTACCTAAAGGTATTTACTCACATAAATTCATCTACCTATGTAATAATCTCTCTC
TCATTCTCTTTAAATATAATACTGAAGATAATAATGAACAAAAAAATCTCTATCTAAGGC
CAATGGATTTAATACTAGATTTTGTGGAATATAAAAATAAGAAGTAGTCGCTAAGCGATA
TATATTGATCTCCCTTCCTCTCTCCCAAATGTTATGTGTTCAAAAATTTTTCCAAATTTT
ATTTTCATACCTATTTATTATATGTAAGAGAAAACTCATTTTATTTCTTGATTAAAATTT
CAATTCATGTATAGTAGTTTTCCGTAGTAATGTGTCTTTTTAACTCAAAAAAAGAATCTA
ACTTCAAGAGAAAAAAAAAGTATGTCGCGATGCAGACAGCAAAGCTTACGTCCAATAAAA
AAATATTTAGAAATGTGAAGAGACATTAAATTTAAATGTATAAGAAAGAAATATTGACTA
TGTATTACTAACTTCCTAAATGTGAAAATGTAAAACGAAGAAAAATTAATAATTAATGAA
AGTGCAAAATGAGAAAAACAATTTTTGAATGGTATTTTAAATATGAGAAATTTATTGATG
AAACGATAAAAAAGAAGAACATTTACAATAGAATTCAAATTTAAATTTTATCATGTTTGA
AAAAGCCAAGTTTGAGAAGTTTTTTTTCTTCCTTTTTTGAATAAAAAAGAAAATAAAACA
TTTACAAAAAAATGAGAGTAATGCTGATGATGTATATATATACTTATTTTTGTAGGTTTT
GAAGCCCTTTTTATAAATTGCATTATATTTTACTTTCTTCTATTTTGCTCAAGTCTTTTC
TTAATATTTATAACCAGTTTACATAATATTATGATAATGAGGTGCTTTTTGGCAGTGAAA
TGTTTTTTATTTTAACTTCTCAACTCACTTTTTCCATATTTCTTTCTTTTTATTGCCTAA
GGCATATTTCAGTTTGACTGTACTTTGAAATATTTCAGCTAAAAGACTTTGAGGTCCT
>g4999.t3 Gene=g4999 Length=213
MTGLLTIIVGAIIQSSYHHYENFIGESFWSAPIILMIVGSLIFFISFLGCCGALRESSCL
ILTFSVFLLFVFITEIGIGVAGYIKHAELPGILERQFNRTLDDYTTSIEAQQAWSLVQGE
LQCCGIYGPLDWKPIFKNKTVPSTCCHILPVNVKNCEVKYSSEEGCYQKLLDFLDTKSLL
LGGVGVGIAIIQLLGVIFACALSRAFRENYETV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g4999.t3 | CDD | cd03127 | tetraspanin_LEL | 83 | 177 | 3.53923E-18 |
| 8 | g4999.t3 | Gene3D | G3DSA:1.10.1450.10 | Tetraspanin | 88 | 176 | 2.5E-10 |
| 2 | g4999.t3 | PANTHER | PTHR19282:SF273 | TETRASPANIN | 1 | 209 | 4.4E-41 |
| 3 | g4999.t3 | PANTHER | PTHR19282 | TETRASPANIN | 1 | 209 | 4.4E-41 |
| 16 | g4999.t3 | PIRSF | PIRSF002419 | Tetraspanin | 1 | 212 | 8.0E-41 |
| 5 | g4999.t3 | PRINTS | PR00259 | Transmembrane four family signature | 28 | 54 | 6.1E-34 |
| 4 | g4999.t3 | PRINTS | PR00259 | Transmembrane four family signature | 55 | 83 | 6.1E-34 |
| 6 | g4999.t3 | PRINTS | PR00259 | Transmembrane four family signature | 180 | 206 | 6.1E-34 |
| 1 | g4999.t3 | Pfam | PF00335 | Tetraspanin family | 2 | 204 | 1.6E-45 |
| 11 | g4999.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 27 | - |
| 14 | g4999.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 48 | - |
| 9 | g4999.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 49 | 59 | - |
| 13 | g4999.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 84 | - |
| 12 | g4999.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 178 | - |
| 15 | g4999.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 202 | - |
| 10 | g4999.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 203 | 213 | - |
| 21 | g4999.t3 | ProSitePatterns | PS00421 | Transmembrane 4 family signature. | 39 | 61 | - |
| 7 | g4999.t3 | SUPERFAMILY | SSF48652 | Tetraspanin | 84 | 177 | 6.15E-15 |
| 18 | g4999.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 28 | 50 | - |
| 19 | g4999.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 84 | - |
| 20 | g4999.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 202 | - |
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 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.
