General information for g1896.t15
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1896 is located on chr_3: 13735448..13739381 (+ 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 | g1896 | g1896.t15 | TSS | g1896.t15 | 13734218 | 13734218 |
| chr_3 | g1896 | g1896.t15 | isoform | g1896.t15 | 13734842 | 13736582 |
| chr_3 | g1896 | g1896.t15 | exon | g1896.t15.exon1 | 13734842 | 13735043 |
| chr_3 | g1896 | g1896.t15 | cds | g1896.t15.CDS1 | 13734856 | 13735043 |
| chr_3 | g1896 | g1896.t15 | exon | g1896.t15.exon2 | 13735107 | 13735126 |
| chr_3 | g1896 | g1896.t15 | cds | g1896.t15.CDS2 | 13735107 | 13735126 |
| chr_3 | g1896 | g1896.t15 | exon | g1896.t15.exon3 | 13735198 | 13735345 |
| chr_3 | g1896 | g1896.t15 | cds | g1896.t15.CDS3 | 13735198 | 13735345 |
| chr_3 | g1896 | g1896.t15 | exon | g1896.t15.exon4 | 13735410 | 13736582 |
| chr_3 | g1896 | g1896.t15 | cds | g1896.t15.CDS4 | 13735410 | 13735581 |
| chr_3 | g1896 | g1896.t15 | TTS | g1896.t15 | 13736528 | 13736528 |
Sequences
>g1896.t15 Gene=g1896 Length=1543
CTATTGATTTATCAATGAATGTAGAACAAAAGGCACCTAAAGTTACCACTGAAGCTCCTA
TTGAAATTTCGGTTTCAATTATGACTTCAGAAACTCCAAAAAAAGATGAACAAGTTACAC
AGATCCCAATTGTTGTTGGAACTGAAATATCAGTAGTAAAGGATCAGGAACAAAAATCAG
TTGACGATAGTGACAACATTTCTACTCCAGATGATACAACAACTTCGACCACATCAACAA
CAAGTGTTTCTCCTCCAAATTCCGATAATACAACAACTACAAGTACCACTACTTCAACCA
CCACAACAACAACACTTGCTCCTGTTCCAGATACTACAACCACTGCTCCAACTACATCCA
CGACACCAACTCCTCTTCCAACAACTACAAAGCCAACTCCTGCACCAGACCATGATCGCT
CGCAATTTTCAGTTACTGCTTTCATTGGAGGAATGGTGTTTGCTTTTGGTATGATGGCAA
TTGGTTTCATTGCTTTTAAGTTCTACAAGGCTCGAAATGAGCGTAATTATCACACTTTGT
AAAGAGAGCTAATCGGAATGGATTACACAACACCTTAATCCATTTTCAATGTAAGAAGCC
ATTTATTAATCAATCTCAAGTGATTTTCCATCGAATATCTTACATATTTTCTTTTTAATC
AAAACTTAATAATCTCGTAATGCTTTTTATATATTTAAATTCTGTTTATTTTTTTAATTT
GTCGTATGATAACGAGATTATCCTATTATTGAATTCTTTTAATATGTCACTATTTTCTAA
ACAGTTTATTCCTATCTAAAGAAATTACACTTACTTATCGATTAGATTTCTACGTAATAT
ATCTCATTTACTTTATTTGATTGATGTTGCAATATAAGGCAGAAGAAAAGCAGCTGAACA
TAAATTTTTCATATCATATAAAAATGTAATCTCAAAATTTAGTAGGAAGAACAAGAATAA
ATATGTAAGTAATAAATACTATGCGTGTATGTAAAGATTATGAAAACGATAGCTATAAAA
TTCTGAAATGCTAAACTATAAGTAATAAGGCAGGTTCTGTTTCACCTAAGAAATAATCTG
CTATTCAAAATTGATAGCTTACTTGTGAAAATTAAGATTTTGCTATGGATAAGATATAAT
CGATGATTGTATGTGAAAAGATGCAATTAAAGCCATTAAATAAATATTATCTCTAATAAA
CCAAGTCTGATTAAAAGATGGTAAAGAAAAATGTGAAGTGCTCTTTTAAAAATAAAATTC
AAAAAAAAAAAAATATTTATGACGAAATGATAAAAAATCTGAAATATTTAAAAGATTTTG
AAAGAAATATAATAAAAAAGATGTAAATTTTAAATTGATTTATTTTTTCAATAATAATAT
TACCTATATAACCATTAAGCTTTTTTGATGTGTAAAAGAATAATATTTAAGCGTTATAAA
TATATAACATACTTTAAGTCATGAATAAAGAAGTTAAAATAAAACAAGATTGGTAATTTT
CAAAAGATTTTTCTCTTTTTTTCATATGTGTATGAAAAAATTT
>g1896.t15 Gene=g1896 Length=175
MNVEQKAPKVTTEAPIEISVSIMTSETPKKDEQVTQIPIVVGTEISVVKDQEQKSVDDSD
NISTPDDTTTSTTSTTSVSPPNSDNTTTTSTTTSTTTTTTLAPVPDTTTTAPTTSTTPTP
LPTTTKPTPAPDHDRSQFSVTAFIGGMVFAFGMMAIGFIAFKFYKARNERNYHTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1896.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 23 | 133 | - |
| 5 | g1896.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 62 | 121 | - |
| 2 | g1896.t15 | PANTHER | PTHR11337 | MUCIN/PORIMIN | 60 | 175 | 9.2E-20 |
| 3 | g1896.t15 | PANTHER | PTHR11337:SF8 | VISGUN, ISOFORM E | 60 | 175 | 9.2E-20 |
| 1 | g1896.t15 | Pfam | PF05283 | Multi-glycosylated core protein 24 (MGC-24), sialomucin | 69 | 175 | 4.8E-10 |
| 8 | g1896.t15 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 137 | - |
| 9 | g1896.t15 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 138 | 161 | - |
| 7 | g1896.t15 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 162 | 175 | - |
| 4 | g1896.t15 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K06546 (CD164 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.
