GPATCH2L (G-Patch Domain Containing 2 Like) is a protein that is encoded by the GPATCH2L human gene located at 14q24.3. In humans, the length of mRNA in GPATCH2L (NM_017926) is 14,021 base pairs and the gene spans bases is 62,422 nt between chr14: 76,151,922 - 76,214,343. GPATCH2L is on the positive strand. IFT43 is the gene directly before GPATCH2L on the positive strand and LOC105370575 is the uncharacterized gene on the negative strand, which is approximately one and a half the size of GPATCH2L. Known aliases for GPATCH2L contain C14orf118, FLJ20689, FLJ10033, and KIAA1152. GPATCH2L produces 28 distinct introns (27 gt-ag, 1 gc-ag), 17 different mRNAs, 14 alternatively spliced variants, and 3 unspliced forms. It has 5 probable alternative promoters, 7 validated polyadenylation sites, and 6 predicted promoters of varying lengths.
Transcript variants There are 23 different transcript variants in GPATCH2L Homo sapiens. The most common is transcript variant 1 and each transcript variant uses different exons.
+ 23 Transcript Variants of GPATCH2L Homo sapiens from NCBI Gene. Name Accession number # of Exons Size (bp) Transcript Variant 1 NM_017926 10 14,021 Transcript Variant 2 NM_017972 9 12,396 Transcript Variant 3, non-coding RNA NR_110314 10 12,511 Transcript Variant 4 NM_001322026 7 3,263 Transcript Variant 5 NM_001322027 4 4,485 Transcript Variant 6 NM_001322028 10 1,797 Transcript Variant 7 NM_001322029 9 1,825 Transcript Variant 8 NM_001322030 10 3,232 Transcript Variant 9 NM_001322031 3 5,278 Transcript Variant 10 NM_001322032 7 3,014 Transcript Variant X1 XM_017021427 11 14,388 Transcript Variant X2 XM_017021428 11 14,373 Transcript Variant X3 XM_017021429 11 3,472 Transcript Variant X4 XM_006720191 10 14,146 Transcript Variant X5 XM_017021430 11 3,457 Transcript Variant X6 XM_017021431 11 2,927 Transcript Variant X7 XM_017021432 11 2,924 Transcript Variant X8 XM_017021433 10 2,685 Transcript Variant X9 XR_001750414 10 14,302 Transcript Variant X10 XR_001750415 10 2,841 Transcript Variant X11 XR_001750416 10 3,386 Transcript Variant X12 XR_001750417 12 1,758 Transcript Variant X13 XR_001750418 12 14,488
Protein The GPATCH2L human protein (NP_060396) has a molecular weight of 54,260 Da and consists of 482 amino acids with a predicted isoelectric point of 8.77. It has 17 different isoforms and the most common is isoform 1. Every human GPATCH2L isoform has a GPATCH2L domain, but no other significant smaller repeats were found as be seen in the schematic illustration below. Also, human GPATCH2L protein in prostate tissue reveals distinct positivity in glandular cells, according to immunohistochemical staining of human prostate GPATCH2L Antibody (HPA018856) in IHC from The Human Protein Atlas.
+ 17 isoforms of GPATCH2L Homo sapiens protein from NCBI Gene. Name Accession number Size (aa) Isoform 1 NP_060396 482 Isoform 2 NP_060442 477 Isoform 4 NP_001308955 434 Isoform 5 NP_001308956 304 Isoform 6 NP_001308957 447 Isoform 7 NP_001308958 446 Isoform 8 NP_001308959 469 Isoform 9 NP_001308960 271 Isoform 10 NP_001308961 402 Isoform X1 XP_016876916 495 Isoform X2 XP_016876917 490 Isoform X3 XP_016876918 482 Isoform X4 XP_006720254 477 Isoform X5 XP_016876919 477 Isoform X6 XP_016876920 460 Isoform X7 XP_016876921 459 Isoform X8 XP_016876922 442
Secondary and tertiary structure
Two figures show the predicted tertiary structure of GPATCH2L human protein from AlphaFold. Four Alpha helix bundles and two Beta sheets are observable and these are annotated on conceptual translation.
Interacting proteins GPATCH2L human protein is known to interact with KRR1, DDX10, and NOL6 within the nucleolus and nucleus.
+ Predicted interacting proteins of GPATCH2L Homo sapiens from STRING. Name Full Name Function Cell's Compartment Experimental Validation String-db Score KRR1 KRR1 small subunit processome component homolog 1) Nucleolar protein required for rRNA synthesis and ribosomal assembly. 2) it enables RNA and protein binding. 3) it is required for 40S ribosome biogenesis in the nucleolus. Nucleolus Experiments: 1) Detected by two-hybrid array assay. 2) Detected by affinity chromatography technology assay. 3) Detected by inferred by author assay. 4) Detected by tandem affinity purification assay. 0.650 DDX10 Probable ATP-dependent RNA helicase DDX10 1) it promotes AIM2-inflammasome activation by maintaining AIM2 protein stability. 2) it promotes human lung carcinoma proliferation by U3 small nucleolar ribonucleoprotein IMP4 Nucleus Experiments: 1) Detected by two-hybrid array assay. 2) Detected by inferred by author assay. 3) Detected by tandem affinity purification assay. 0.548 NOL6 Nucleolar protein 6 A nucleolar RNA-associated protein; 1) it is related to ribosome biogenesis in endometrial cancer. 2) it promotes the proliferation and migration of endometrial cancer cells by regulating TWIST1 expression. Nucleus Experiments: 1) Detected by two-hybrid array assay. 2) Detected by inferred by author assay. 3) Detected by tandem affinity purification assay. 0.527
Gene level regulation Promoter GPATCH2L human gene has a promoter [GXP_207451] located in ch14:76150912 - 76151972. The length of the promoter is 1061 bp.
Transcription factor binding sites 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. 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.
+ Detailed information about 20 transcription factors in human GPATCH2L from Genomatix. Element Description/Full Name The Best Matrix Score The Number of Binding Sites in The Region AP1F AP1, Activating protein 1 0.903 1 NR2F Nuclear receptor subfamily 2 factors 0.826 5 LHXF Lim homeodomain factors 0.906 3 STAT Signal transducer and activator of transcription 0.896 2 HIFF Hypoxia inducible factor, bHLH/PAS protein family 0.989 5 HESF Vertebrate homologues of enhancer of split complex 0.985 2 KLFS Krueppel like transcription factors 0.912 13 GLIF GLI zinc finger family 0.914 5 PLAG Pleomorphic adenoma gene 0.845 4 SP1F GC-Box factors SP1/GC 0.855 9 EGRF EGR/nerve growth factor-induced protein C & related factors 0.930 4 HOMF Homeodomain transcription factors 0.980 5 CAAT CCAAT binding factors 0.926 1 AP2F Activator protein 2 0.917 1 ZF02 C2H2 zinc finger transcription factors 2 0.932 3 RXRF RXR heterodimer binding sites 0.850 9 SMAD Vertebrate SMAD family of transcription factors 0.994 2 CREB cAMP-responsive element binding proteins 0.844 6 NFKB Nuclear factor kappa B/c-rel 0.928 4 MAZF Myc associated zinc fingers 1.000 3
Transcript level regulation
Expression Pattern RNA-seq was performed on tissue samples from 95 human individuals representing 27 different tissues to identify tissue-specificity protein-coding genes at NCBI. 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.
NCBI GEO profile across all tissues
Significantly different gene expressions in tissues are shown in a microarray-assessed tissue expression pattern (GDS596) in GPATCH2L Homo sapiens from NCBI GEO. 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. 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.
+ Three highest values among 158 samples in a microarray-assessed tissue expression pattern (GDS596) in GPATCH2L Homo sapiens from NCBI GEO. Sample/Tissue Title Value Rank GSM19012 / (Superior Cervical Ganglion) 3AJZ02081478b_Superior_Cervical_Ganglion 1408.7 81 GSM19014 / (Skeletal Muscle) 3AJZ02083092b_Skeletal_Muscle_Psoas 819.2 83 GSM19009 / (Dorsal Root Ganglion) 3ARS02080736e_DRG 787.4 81
+ Three lowest values among 158 samples in a microarray-assessed tissue expression pattern (GDS596) in GPATCH2L Homo Sapiens from NCBI GEO. Sample/Tissue Title Value Rank GSM18875 / (PB-CD 56+NK cells) / (Superior Cervical Ganglion) 3AMH02082109_PB_CD56NKCells 10.1 19 GSM18969 / (Cardiac Myocytes) 3AJZ02053107_CardiacMyocytes 10.1 12 GSM18881 / (PB - CD 19 + B cells) 3AMH02082107_PB_CD19BCells 10.5 28
Predicted stem-loops and miRNA targeting 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.
Protein level regulation
Immunochemistry (IHC)
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. 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.
Protein localization and abundance
GPATCH2L Homo sapiens protein is mainly localized to the nucleoplasm, according to GPATCH2L antibody staining from The Human Protein Atlas and Thermo Fisher Scientific. Also, 82.6% of GPATCH2L human protein is predicted to be located in the nucleus, according to PSORT II and pI/MW tool from Expasy. GPATCH2L human protein is Isoleucine poor (I−), Serine rich (S+), and Arginine rich (R+) compared to other human proteins. 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.
Homology and evolution
Orthologs and paralogs 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. 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(%)).