The PTPRD gene is composed of 36 coding sequence exons and a 5 UTR spliced together from 11 non-coding exons.

There are five known transcript variants for PTPRD.
Transcript Variant 1: This variant encodes the longest isoform 1 and is 10078 bp in length (Figure A).
Transcript Variant 2: This variant lacks two separate internal segments within the coding region. It thus encodes a protein that lacks a 9 aa, and a 4 aa internal fragments, as compared to isoform 1 and is 10039 bp in length (Figure C).
Transcript Variant 3: This variant lacks an internal segment within the coding region. It thus encodes a protein that lacks a 9 aa internal fragment, as compared to isoform 1 and is 10051 bp in length (Figure D).
Transcript Variant 4: This variant lacks an internal segment within the coding region. It thus encodes a protein that lacks a 411 aa internal fragment, and has one amino acid change, as compared to isoform 1 and is 8845 bp in length (Figure B).
Transcript Variant 5: This variant omits several exons, and utilizes an alternate exon, in the coding region. The resulting protein (isoform 5) retains the same reading frame and has the same N- and C-terminus as isoform 1. This variant is 8848 bp in length (Figure E).

No pseudogenes have been reported.

Amino acids: 1912.
Molecular Weight: 214760 Da.
The PTPRD gene belongs to the receptor class 2A subfamily of the protein-tyrosine phosphatases. It contains an extracellular region composed of 8 fibronectin type-III domains and 3 Ig-like C2-type (immunoglobulin-like) domains, a single transmembrane segment and two tandem intracytoplasmic tyrosine-protein phosphatase domains.
Molecular Class: Receptor Tyrosine Phosphatase.
Molecular Function: Receptor Signalling Protein Tyrosine Phosphatase Activity.
Biological Process: Cell Communication ; Signal Transduction.

Brain, Kidney.
Multiple isoforms are generated by either alternate splicing or by alternate transcriptional start sites in a tissue specific manner. The predominant isoform in brain has an extended 711 base pair 5 UTR (L isoform), while the isoform (S) expressed in kidney lacks the extended 5 UTR. In addition, the brain isoform is characterized by the absence of exons 14 to 18 corresponding to amino acid residues 568 to 978 of the 4^th through 7^th fibronectin III-like domain and by the insertion of a 12 base pair mini-exon sequence between exons 23 and 24 (Nair et al., 2008).
The full length PTPRD isoform has an extracellular region containing three Ig-like and eight FN-III like domains connected via a transmembrane peptide to an intracellular region with two PTPase domains (A), whereas another isoform lacks four of the eight FN-III like domains (B). Furthermore, other PTPRD isoforms exist that lack 9 AA within the second Ig-like domain and 4 AA at the junction of the 2^nd and 3^rd Ig-like domains (C) or 9 AAs within the 5^th FN-III like domain (D). The fifth isoform lacks four of the eight FN-III like domains and has mutation in the second Ig-like domain (E). RT-PCR analysis demonstrated that PTPRD isoforms lacking these short peptides are expressed in kidney, whereas isoforms containing these peptides are expressed in the brain (Pulido et al., 1995).

Membrane; Single-pass type I membrane protein.

A cleavage occurs, separating the extracellular domain from the transmembrane segment. This process called ectodomain shedding is thought to be involved in receptor desensitization, signal transduction and/or membrane localization. Plays key role in promoting neurite growth and regulating axon guidance.

PTPRD shares a PTP domain, involved in dephosphorylating phosphorylated tyrosine residues, with the other receptor-like protein tyrosine phosphatases. The human and mouse PTPRD sequences are 93% identical and 95% homologous.