General information for g1896.t1
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.t1 | TSS | g1896.t1 | 13734218 | 13734218 |
| chr_3 | g1896 | g1896.t1 | isoform | g1896.t1 | 13734316 | 13735581 |
| chr_3 | g1896 | g1896.t1 | exon | g1896.t1.exon1 | 13734316 | 13734388 |
| chr_3 | g1896 | g1896.t1 | cds | g1896.t1.CDS1 | 13734316 | 13734388 |
| chr_3 | g1896 | g1896.t1 | exon | g1896.t1.exon2 | 13734842 | 13735043 |
| chr_3 | g1896 | g1896.t1 | cds | g1896.t1.CDS2 | 13734842 | 13735043 |
| chr_3 | g1896 | g1896.t1 | exon | g1896.t1.exon3 | 13735107 | 13735126 |
| chr_3 | g1896 | g1896.t1 | cds | g1896.t1.CDS3 | 13735107 | 13735126 |
| chr_3 | g1896 | g1896.t1 | exon | g1896.t1.exon4 | 13735198 | 13735345 |
| chr_3 | g1896 | g1896.t1 | cds | g1896.t1.CDS4 | 13735198 | 13735345 |
| chr_3 | g1896 | g1896.t1 | exon | g1896.t1.exon5 | 13735410 | 13735581 |
| chr_3 | g1896 | g1896.t1 | cds | g1896.t1.CDS5 | 13735410 | 13735581 |
| chr_3 | g1896 | g1896.t1 | TTS | g1896.t1 | 13736528 | 13736528 |
Sequences
>g1896.t1 Gene=g1896 Length=615
ATGAAGAACTATGGCATAGCTCTTGCTTTATTGTGCATTTTGAGTGCTCAATTAGTATAT
TCGGCTCCGAATACTATTGATTTATCAATGAATGTAGAACAAAAGGCACCTAAAGTTACC
ACTGAAGCTCCTATTGAAATTTCGGTTTCAATTATGACTTCAGAAACTCCAAAAAAAGAT
GAACAAGTTACACAGATCCCAATTGTTGTTGGAACTGAAATATCAGTAGTAAAGGATCAG
GAACAAAAATCAGTTGACGATAGTGACAACATTTCTACTCCAGATGATACAACAACTTCG
ACCACATCAACAACAAGTGTTTCTCCTCCAAATTCCGATAATACAACAACTACAAGTACC
ACTACTTCAACCACCACAACAACAACACTTGCTCCTGTTCCAGATACTACAACCACTGCT
CCAACTACATCCACGACACCAACTCCTCTTCCAACAACTACAAAGCCAACTCCTGCACCA
GACCATGATCGCTCGCAATTTTCAGTTACTGCTTTCATTGGAGGAATGGTGTTTGCTTTT
GGTATGATGGCAATTGGTTTCATTGCTTTTAAGTTCTACAAGGCTCGAAATGAGCGTAAT
TATCACACTTTGTAA
>g1896.t1 Gene=g1896 Length=204
MKNYGIALALLCILSAQLVYSAPNTIDLSMNVEQKAPKVTTEAPIEISVSIMTSETPKKD
EQVTQIPIVVGTEISVVKDQEQKSVDDSDNISTPDDTTTSTTSTTSVSPPNSDNTTTTST
TTSTTTTTTLAPVPDTTTTAPTTSTTPTPLPTTTKPTPAPDHDRSQFSVTAFIGGMVFAF
GMMAIGFIAFKFYKARNERNYHTL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g1896.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 162 | - |
| 15 | g1896.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 91 | 150 | - |
| 2 | g1896.t1 | PANTHER | PTHR11337 | MUCIN/PORIMIN | 6 | 204 | 2.9E-22 |
| 1 | g1896.t1 | Pfam | PF05283 | Multi-glycosylated core protein 24 (MGC-24), sialomucin | 98 | 204 | 1.5E-9 |
| 7 | g1896.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 8 | g1896.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 9 | g1896.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 16 | - |
| 11 | g1896.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 6 | g1896.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 166 | - |
| 10 | g1896.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 190 | - |
| 5 | g1896.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 191 | 204 | - |
| 4 | g1896.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 12 | g1896.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 3 | g1896.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 21 | - |
| 13 | g1896.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 190 | - |
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.
