General information for g16947.t3
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.t3 | TTS | g16947.t3 | 11848629 | 11848629 |
| chr_4 | g16947 | g16947.t3 | isoform | g16947.t3 | 11848678 | 11850861 |
| chr_4 | g16947 | g16947.t3 | exon | g16947.t3.exon1 | 11848678 | 11848826 |
| chr_4 | g16947 | g16947.t3 | cds | g16947.t3.CDS1 | 11848738 | 11848826 |
| chr_4 | g16947 | g16947.t3 | exon | g16947.t3.exon2 | 11849817 | 11850031 |
| chr_4 | g16947 | g16947.t3 | cds | g16947.t3.CDS2 | 11849817 | 11850031 |
| chr_4 | g16947 | g16947.t3 | exon | g16947.t3.exon3 | 11850424 | 11850677 |
| chr_4 | g16947 | g16947.t3 | cds | g16947.t3.CDS3 | 11850424 | 11850677 |
| chr_4 | g16947 | g16947.t3 | exon | g16947.t3.exon4 | 11850733 | 11850861 |
| chr_4 | g16947 | g16947.t3 | cds | g16947.t3.CDS4 | 11850733 | 11850861 |
| chr_4 | g16947 | g16947.t3 | TSS | g16947.t3 | 11850930 | 11850930 |
Sequences
>g16947.t3 Gene=g16947 Length=747
ATGGAAAACAGAAAGGCAATGATGATATCAGTGACAATTCTTGGAATATCAATTTTAATA
GTTTTATTTGCTTATGTTGCATTTGGTGACAATACGGATGAAGATATGAAAACTTTGCAA
CAAGTGAATATCATCTTCAGACATGGTGCAAAATATCCTGACAAAACTTATAGAAAAGAT
TTTTACCTCAATGAAGTTCAAAATCACGATCCTGGTTCATTAACAAATTATGGAAGTCTT
CAAATGTACAATTTAGGAAAGAATTTGAGACATCGATATTTAAAATTGCTGCCTCAAAAT
GGATTTTATACAAATAAAGTTATTTCAGTGAAATCCAGTTGGAAAGATCGAACTATTATG
AGTGCACAATCTTTTCTGGCTGGTTTTATGCCACCACTCGATAATAAAAATCCTCTTCCC
ATCCCTTGGCAGCCAATTCCAATTTATACAATTCCAAGAAATATTGATGATCTTATAGCA
CAAAAGCGTTATTGTCCAAAATATAATGAAGTTTATAACGAACTAATGAAATCAGAAGAA
ATCAAAAAACTTGATGAAACAAATCAACCGCTTTATAGAATTTTATCAGTAAATACAGGC
TACTTCATGCAAATTATCAAAAAACTATCAAAAATCTCTTACAAATTTTTGATACTTTTT
TTGATAGAGTTCACACACCTTGGCTAATGCAAAATAGTTTCAAAAACTTTCGAAAACAAA
GAAAAAACACCAAAAATTTTATAAAAT
>g16947.t3 Gene=g16947 Length=228
MENRKAMMISVTILGISILIVLFAYVAFGDNTDEDMKTLQQVNIIFRHGAKYPDKTYRKD
FYLNEVQNHDPGSLTNYGSLQMYNLGKNLRHRYLKLLPQNGFYTNKVISVKSSWKDRTIM
SAQSFLAGFMPPLDNKNPLPIPWQPIPIYTIPRNIDDLIAQKRYCPKYNEVYNELMKSEE
IKKLDETNQPLYRILSVNTGYFMQIIKKLSKISYKFLILFLIEFTHLG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g16947.t3 | CDD | cd07061 | HP_HAP_like | 38 | 157 | 3.20852E-25 |
| 6 | g16947.t3 | Gene3D | G3DSA:3.40.50.1240 | - | 37 | 223 | 9.0E-47 |
| 2 | g16947.t3 | PANTHER | PTHR11567 | ACID PHOSPHATASE-RELATED | 3 | 209 | 1.5E-73 |
| 3 | g16947.t3 | PANTHER | PTHR11567:SF19 | GH19849P | 3 | 209 | 1.5E-73 |
| 1 | g16947.t3 | Pfam | PF00328 | Histidine phosphatase superfamily (branch 2) | 72 | 177 | 5.3E-13 |
| 8 | g16947.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 29 | - |
| 9 | g16947.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 10 | g16947.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 24 | - |
| 11 | g16947.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 25 | 29 | - |
| 7 | g16947.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 30 | 228 | - |
| 4 | g16947.t3 | SUPERFAMILY | SSF53254 | Phosphoglycerate mutase-like | 38 | 200 | 4.42E-41 |
| 5 | g16947.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 29 | - |
| 13 | g16947.t3 | 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 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.
