

An In-Depth Analysis of Neuropilin 1
Nicole Dano and Jessica Hrnciar
Date Published: December, 14 2020
General Information
Gene name: Neuropilin 1
Official symbol: NRP1
Also known as: NP1, NRP, BDCA4, CD304, VEGF165R
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Genomic location: 33177493-33334667
Cytogenic location: 10p11.22
Genomic build: GRCh38.p13
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All of the protein and nucleic acid sequence detailed information used was found through the NCBI AceView database (8).
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The diagrams and tables we created about the NRP1 gene are all based on information from AceView. AceView lists 30 isoforms of which 23 are alternatively spliced variants and 7 are unspliced variants. The isoforms are labeled a-u and va-vi. We decided to focus on two specific isoforms and more information about them is shown on the isoform page.
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Gene Diagram
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NCBI RefSeq genome (3): NC_000010.11
NCBI RefSeq isoform a (4): NM_003873.7
NCBI RefSeq isoform I (5):
NCBI RefSeq isoform a protein (6): NP_003864.5
NCBI RefSeq isoform i
protein (7): NP_001019800.2

This gene diagram was created based on information from AceView. Information about promoter region features was found using EPD.
The NRP1 gene has a total of 71 exons and 33 introns, along with 16 Poly A sites. In an effort to make a neat and understandable gene diagram we did not include all of these features and we purposely chose features we thought were important. We only included exons that contained the sequences that code for the domains found in our protein. These domains include CUB domain, F5/8 type C domain, MAM domain, and transmembrane domain. We also chose exons that were found in at least 3 of the isoforms. We also included all of the exons that were in the two isoforms that we chose to later explain, isoform a and isoform i. The Poly-A sites we chose to include were the ones that occurred in the last exon and we also included the Poly A site for isoform i since that is one of the isoforms we chose to focus on in our isoform page.
Our gene has 4 transcription start sites which are all included in the diagram along with all of the initiator, TATA box, GC box and CCAAT box locations. Overlapping exons are represented by a normal exon block with a darker exon block within it. Introns greater than 5000bps are represented with breaks to save space on the diagram (8,9).
NRP1 Gene Table




The information from this table is mainly from AceView (8). However, it is important to note that similar to the gene diagram we did not include all of the possible introns and exons. We only chose the introns and exons we included in our diagram. The features that are present before the TSS are obtained from EPD (9). Our gene has 4 promoters; we took the CCAAT Box, GC Box, TATA Box, and Initiator locations of all 4 promoters and compared their absolute location. Once we did this, we found that all four TSS had essentially the same locations for these features.
Expression
Tissue Expression of NRP1

Overall, NRP1 is expressed 5.3 times the average gene in this release, according to AceView (8). This gene is expressed in many different tissue types, with the most prominent locations being the colon, lung, lymph node, heart, and kidney. On top of this, each individual variant has its own individual expression pattern. The image above is directly from AceView (8).
Isoform Specific Tissue Expression
a
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uterus
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breast
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coronary artery
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Thalamus
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74 others
e
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endometrium caarcinoma cell line
i
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adenocarcinoma cell line
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placenta cot
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breast
-
liver
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prostate
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muscle
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rhabdomyosarcoma
b
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brain
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trachea
c
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lung
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kidney
-
uterus
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pancreas
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88 others
f
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bone
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breast
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hypernephroma
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kidney
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liver
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osteosarcoma
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embryo
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prostate adenocarcinoma
g
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uterus
-
bone
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fibrosarcoma
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hip
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13 others
j
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-
prostate
k
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pancreas
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pancreatic islet
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pooled human melanocyte
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fetal heart
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pregnant uterus
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adenocarcinoma cell line
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8 others
d
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leiomios
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thymus
h
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dorsal root ganglia
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lung
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placenta
l
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Corpus callosum
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embryonic stem cells
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embryoid bodies
m
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colon
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rough ER
q
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carcinoid
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lung
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epithelium
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ovary
u
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bone marrow stroma
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knee
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osteoarthritic cartilage
vd
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hypothalamus
n
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none listed
o
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kidney
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pooled chondrosarcoma tumor cells
r
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eye
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fetal eyes
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skeletal muscle
s
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none listed
p
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-
none listed
t
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adenocarcinoma
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colon
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stomach
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skeletal muscle
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spleen
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lung
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testis
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small intenstines
va
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brain
vb
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adipose
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prostate
ve
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hippocampus
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hypothalamus
vf
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none listed
vc
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liver
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spleen
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placenta
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anaplastic oligodendroglioma
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brain
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sciatic nerve
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neuroblastoma
vg
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bone
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subchondral bone
vh
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placenta
vi
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none listed
The boxes above are a summary of tissue-specific expression for all of the Neuropilin-1 isoforms. The information was collected from AceView, however, some isoforms did not have any tissue expressions listed (8). We were surprised to find that even some of the unspliced isoforms were found to be heavily expressed in certain tissues. Similar to the overall gene expression, most isoforms seem to commonly be expressed in the kidney, colon, and lungs. One of the physiological states that a few of our isoforms seem to be expressed in is fetal development. For example, isoform r is expressed in the fetal eye and the majority of the eye structures, and isoform k is expressed in the fetal heart and pregnant uterus. In addition to fetal development, many isoforms were found in cancerous tissues. For example, isoform vc is found in anaplastic oligodendroglioma tissue, which is a rare form of brain cancer. In summary, the most common physiological states that the isoforms are expressed in are fetal development and cancerous tissue.
Development Related Differential Gene Expression
During different stages of human development NRP1 tissue specific expression changes. Ensembl has a specific section for gene expression, and within that section the gene expression is broken down into expression at different developmental stages (10). For NRP1 Ensembl specifically listed developmental stages of the brain post conception. NRP1 gene expression 9 weeks post conception was highest in the pons, with an expression level of 82 TPM, and next was the spinal cord at 53 TPM. Other notable expression areas of the brain at 9 weeks post conception are the basal ganglion, diencephalon, midbrain, medulla oblongata, midbrain, and telencephalon, all of which had expression above 20 TPM. Later on at 16 weeks post conception, NRP1 is highly expressed in the hippocampus, with an expression level of 130 TPM. Also, in this stage the expression in the brain fragment, midbrain, and pons are all above 30 TPM. At an even later development stage, 19 weeks post conception the NRP1 expression is only in the brain fragment with an expression level of 59 TPM. Although Ensembl only provided detailed development stages for the brain it also provided data for NRP1 expression in the fetal human proteome (10). Interestingly, the brain was not where the highest NRP1 expression was located; the fetal heart had the highest expression level. This fetal proteome also revealed that NRP1 is expressed in the gut, liver, and testis during human development.