General information for g16947.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Lysosomal acid phosphatase.
Parent gene
- The parent gene g16947 is located on chr_4: 11849269..11850861 (- 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_4 | g16947 | g16947.t1 | TTS | g16947.t1 | 11848629 | 11848629 |
| chr_4 | g16947 | g16947.t1 | isoform | g16947.t1 | 11849269 | 11850861 |
| chr_4 | g16947 | g16947.t1 | exon | g16947.t1.exon1 | 11849269 | 11850031 |
| chr_4 | g16947 | g16947.t1 | cds | g16947.t1.CDS1 | 11849269 | 11850031 |
| chr_4 | g16947 | g16947.t1 | exon | g16947.t1.exon2 | 11850424 | 11850677 |
| chr_4 | g16947 | g16947.t1 | cds | g16947.t1.CDS2 | 11850424 | 11850677 |
| chr_4 | g16947 | g16947.t1 | exon | g16947.t1.exon3 | 11850733 | 11850861 |
| chr_4 | g16947 | g16947.t1 | cds | g16947.t1.CDS3 | 11850733 | 11850861 |
| chr_4 | g16947 | g16947.t1 | TSS | g16947.t1 | 11850930 | 11850930 |
Sequences
>g16947.t1 Gene=g16947 Length=1146
ATGGAAAACAGAAAGGCAATGATGATATCAGTGACAATTCTTGGAATATCAATTTTAATA
GTTTTATTTGCTTATGTTGCATTTGGTGACAATACGGATGAAGATATGAAAACTTTGCAA
CAAGTGAATATCATCTTCAGACATGGTGCAAAATATCCTGACAAAACTTATAGAAAAGAT
TTTTACCTCAATGAAGTTCAAAATCACGATCCTGGTTCATTAACAAATTATGGAAGTCTT
CAAATGTACAATTTAGGAAAGAATTTGAGACATCGATATTTAAAATTGCTGCCTCAAAAT
GGATTTTATACAAATAAAGTTATTTCAGTGAAATCCAGTTGGAAAGATCGAACTATTATG
AGTGCACAATCTTTTCTGGCTGGTTTTATGCCACCACTCGATAATAAAAATCCTCTTCCC
ATCCCTTGGCAGCCAATTCCAATTTATACAATTCCAAGAAATATTGATGATCTTATAGCA
CAAAAGCGTTATTGTCCAAAATATAATGAAGTTTATAACGAACTAATGAAATCAGAAGAA
ATCAAAAAACTTGATGAAACAAATCAACCGCTTTATAGAATTTTATCAGTAAATACAGGT
GAAAATATTAGCAATCTTTTGCAAGTTGAATTGTTGCACAACACATTAGAAGCTGAAAAA
GTAGCTGGATGGAATTTACCTGATTTTCTTGAAGGAATTTTTCCACAAAAAACTTTGCCA
ATAGCTGAAAAATATTTGAGATTAATAACAGAAACTCCATTTATGAAAAGAATTAAAGCT
GGTCCATTGACAAGTGAAATTATTGAAAATATGTTCAATAAACGAAATAATTTACCTACT
GAAAAATCAATCAATATTTATTCAGCTCATGATGTGACACTTGTAAATTTAATGAATTCA
ATGAATTTTTTGGATCAAACAACAAATAAGCCAGATTTTTCATCTGCATTGGCAATTGAA
TTGCATAGCAGTTATTCAAGTGTTGATATGGATGTGAAAATTTATTATTATTTTAATTCT
GATGACAAATATCCAAAAGTTATTAAAATTAAAGATTGTGAAGATCCTTGTCCATTGAAT
ACATTTAGAAAAGTCATGAATCATTTGATTGTTAATGATTTTGAGAAACTTTGTGAGACT
GTTTAA
>g16947.t1 Gene=g16947 Length=381
MENRKAMMISVTILGISILIVLFAYVAFGDNTDEDMKTLQQVNIIFRHGAKYPDKTYRKD
FYLNEVQNHDPGSLTNYGSLQMYNLGKNLRHRYLKLLPQNGFYTNKVISVKSSWKDRTIM
SAQSFLAGFMPPLDNKNPLPIPWQPIPIYTIPRNIDDLIAQKRYCPKYNEVYNELMKSEE
IKKLDETNQPLYRILSVNTGENISNLLQVELLHNTLEAEKVAGWNLPDFLEGIFPQKTLP
IAEKYLRLITETPFMKRIKAGPLTSEIIENMFNKRNNLPTEKSINIYSAHDVTLVNLMNS
MNFLDQTTNKPDFSSALAIELHSSYSSVDMDVKIYYYFNSDDKYPKVIKIKDCEDPCPLN
TFRKVMNHLIVNDFEKLCETV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g16947.t1 | CDD | cd07061 | HP_HAP_like | 38 | 336 | 1.18038E-31 |
| 7 | g16947.t1 | Coils | Coil | Coil | 371 | 381 | - |
| 6 | g16947.t1 | Gene3D | G3DSA:3.40.50.1240 | - | 37 | 381 | 3.8E-83 |
| 2 | g16947.t1 | PANTHER | PTHR11567 | ACID PHOSPHATASE-RELATED | 3 | 379 | 4.9E-137 |
| 3 | g16947.t1 | PANTHER | PTHR11567:SF19 | GH19849P | 3 | 379 | 4.9E-137 |
| 1 | g16947.t1 | Pfam | PF00328 | Histidine phosphatase superfamily (branch 2) | 72 | 180 | 8.9E-13 |
| 9 | g16947.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 29 | - |
| 10 | g16947.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 11 | g16947.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 24 | - |
| 12 | g16947.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 25 | 29 | - |
| 8 | g16947.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 381 | - |
| 4 | g16947.t1 | SUPERFAMILY | SSF53254 | Phosphoglycerate mutase-like | 38 | 378 | 5.72E-72 |
| 5 | g16947.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 29 | - |
| 14 | g16947.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
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 K14410 (lysosomal acid phosphatase)
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.
