GPATCH2L

Two figures show the predicted tertiary structure of GPATCH2L human protein from AlphaFold.[11] Four Alpha helix bundles and two Beta sheets are observable and these are annotated on conceptual translation.

The GPATCH2L domain annotated in yellow is shown on the predicted tertiary structure from AlphaFold[11] by using iCn3D viewer from NCBI.[6]

GPATCH2L human protein is known to interact with KRR1, DDX10, and NOL6 within the nucleolus and nucleus.

GPATCH2L human gene has a promoter [GXP_207451] located in ch14:76150912 - 76151972.[13] The length of the promoter is 1061 bp.

In the below table , 5 transcription factors [KLFS, HOMF, SP1F, ZF02, and NFKB] are predicted to bind within a conserved section of the transcriptional regulatory region. Unlike 19 transcription factors in the table, MAZF is only specifically active in cartilage and skeleton tissues.[13] Also, PLAG is only specifically active in bone marrow cells, digestive system, embryonic structures, endocrine system, germ cells, and hematopoietic system. Most transcription factors are active in the ovary, lung, brain, prostate, bone marrow cells, which show the highest values in RNA-seq data from the Gene database record at NCBI.[6]

The multiple sequence alignment of GPATCH2L mammals shows NFKB is the most conserved transcription factor.

RNA-seq was performed on tissue samples from 95 human individuals representing 27 different tissues to identify tissue-specificity protein-coding genes at NCBI.[6] RNA-seq data shows high expression within the bone marrow, testis, and brain tissue in GPATCH2L human mRNA. Tissues with low expression are the pancreas, liver, and salivary glands.

Human GPATCH2L mRNA level in lung carcinoma and all normal tissues, including lung tissue, on average from NCBI GEO.[14]

Significantly different gene expressions in tissues are shown in a microarray-assessed tissue expression pattern (GDS596) in GPATCH2L Homo sapiens from NCBI GEO.[14] The high gene expressions in cerebellum, fetal brain, bone marrow, ovary, prostate, and lung tissues in RNA-seq data are extremely low in GDS596. However, the gene expressions in liver, pancreas, salivary gland, and fetal liver tissues remain low in every gene database record.

A graph in NCBI GEO can be interpreted as follows: a 'single channel' sample means that a hybridization where cDNA obtained from one biosource is combined with the array.[14] This method is typically used for membrane (filter) arrays with radionucleotide labels and high-density oligonucleotide arrays with fluorescent labels. This experiment type makes the measurements of gene expression, which are defined as scaled/normalized signal count values that correspond to "value" in the below tables and right figures.

The nucleic acid secondary structure of human GPATCH2L (5’UTR) shows one stem-loop, inframe stop codon, start codon, and exon boundaries. In this stem-loop, g and g are not connected. However, these are conserved in the multiple sequence alignment of this stem-loop region. In the 3'UTR figure, there are 10 stem-loops and these are zoomed in another figure. Although 3-3), 3-6), 3-9) show weird structure (3: CCTT, 6: CAT, TTC, 9:GTG), every letter is conserved in its multiple sequence alignment. Especially, 3-8) includes hsa-miRNA-205 in its stem-loop, and every letter of hsa-miRNA-205 is conserved in the multiple sequence alignment.

GPATCH2L protein is highly expressed in the bone marrow tissues, according to immunohistochemical staining of human hematopoietic cells in bone marrow tissue GPATCH2L Antibody (HPA018856) in IHC from The Human Protein Atlas.[9] Also, it has shown that GPATCH2L protein is highly expressed in human respiratory epithelial cells in bronchus tissue and human cells in endometrial stroma and glandular cells in endometrium tissue.

GPATCH2L Homo sapiens protein is mainly localized to the nucleoplasm, according to GPATCH2L antibody staining from The Human Protein Atlas and Thermo Fisher Scientific.[9][15] Also, 82.6% of GPATCH2L human protein is predicted to be located in the nucleus, according to PSORT II[16] and pI/MW tool from Expasy.[8] GPATCH2L human protein is Isoleucine poor (I-), Serine rich (S+), and Arginine rich (R+) compared to other human proteins.[17] The post-translational modification sites [O-GalNAc (mucin-type) glycosylation, 0-(beta)-GlcNAc, N-glycosylation, O-glycosylation, and phosphorylation] are annotated on the conceptual translation. The conceptual translation figures in Wikipedia only include 1,560 bp mRNA and 482 amino acids.

Human GPATCH2L isoform 1 (NM_017926.4) annotated conceptual translation 1

Human GPATCH2L isoform 1 (NM_017926.4) annotated conceptual translation 2

GPATCH2L Homo sapiens has orthologs in Mammalia, Reptilia, Amphibia, Mollusca, Arthropoda, Ave, Fish, and Invertebrate. The values [query cover values (%), sequence identity (%), and sequence similarity (%)] decrease as the group changes into more distant orthologs from Homo sapiens, such as Invertebrates. However, frogs are unusual in that they have a very low sequence identity (36.8% - 38.0%). Also, the class of fungi and bacteria that contain GPATCH2L homologs was not able to be found using NCBI Homologene.[18] The paralogs of GPATCH2L Homo sapiens were found by using NCBI Homologene. In the below table, MYA stands for "Million Years Ago" and the equation of the corrected divergence [m] is 100*(-LN(sequence similarity(%)).

GPATCH2L evolves more slowly compared to Fibrinogen Alpha Chain but faster than Cytochrome C.[19] In the unrooted tree of GPATCH2L protein, only one mammal (human) is included since every species in mammals is very closely related to each other, showing various short lines. Arthropoda in invertebrates shows the longest line, meaning that they have diverged the longest.

GPATCH2L Homo sapiens evolutionary graph

An unrooted tree of GPATCH2L protein, including Mammal, Bird, Reptile, Arthropoda, Mollusca, Annelida, Amphibians, and Fish, was created by using LIRMM.[20]

The closest organisms that do/do not have GPATCH2L are as follows: In reptiles, GPATCH2L homologs in crocodile, turtle, snake, lizard, gecko were found by using NCBI Blast,[21] while there were no homologs in skink, chameleon,and iguana. In amphibians, GPATCH2L homologs in frog, toad, and salamander were found by using NCBI Blast,[21] while other types of amphibians, such as caecilian, microsauria, and labyrinthodontia, do not contain GPATCH2L gene. In Invertebrates, NCBI Blast[21] demonstrates that scallop, starfish, octopus, spider have GPATCH2L gene, but sponge and jellyfish do not. Lastly, there are no GPATCH2L homolog in fungi and bacteria, according to NCBI Blast.[21]

The analysis of amino acids in GPATCH2L human with distant homologs [ant, honeybee, acorn barnacle, octopus, and snail].