RetrogeneDB ID:

retro_hsap_4085

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:85740810..85741209(-)
Located in intron of:ENSG00000184672
Retrocopy
information
Ensembl ID:ENSG00000248978
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GNPNAT1
Ensembl ID:ENSG00000100522
Aliases:GNPNAT1, GNPNAT, Gpnat1
Description:glucosamine-phosphate N-acetyltransferase 1 [Source:HGNC Symbol;Acc:19980]


Retrocopy-Parental alignment summary:






>retro_hsap_4085
AACCTAGGGTTTTTTTTTTTTAAGGTAGTGGGTCAGCGAACTGCCACTGGAGTTGTCAACCTTGATAATGTATAAAGCAT
TTTGAGCATACAAAGAAATCTGTGGTTCATTATGTTACAGTTGTGGAAGATGTGACTCGGTGACAGTGTTGCCATGACAA
CTCTGATAATAGTACATAAATTCATCCTTTCCTGTGCTAAGAGAGAAAGAGTAGATGTTGTTAGCAGTGAATGCAGAGGA
AGACAGCTTGGCAAATTGTTATCAACTTGTAGTTTGCTAAGCAAGAAACTGAACTGTTATAAGATTACTCTTGAATGTCT
ACCACAAAATGTTGGTTTTTACAAAACATTTGGATACATTGGATCTGAAGAAAACTACATATGTCAGAGGTTTCTAAAG

ORF - retro_hsap_4085 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.19 %
Parental protein coverage: 74.46 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDLNRGFFKVLGQLTETGVVSPEQF-MKSFEHMKKSGDYYVTVVEDVTLGQ-IVATATLIIEHKFIHSCAK
.L.....KV.GQ.T.TGVV.......K.FEH.KKS...YVTVVEDVT..Q....T...I..HKFI.SCAK
RetrocopyNLGXXXXKVVGQRTATGVVNLDNV<IKHFEHTKKSVVHYVTVVEDVTR*Q>VAMTTLIIV-HKFILSCAK
ParentalRGRVEDVVVSDECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRFLK
R.RV...VVS.ECRG.QLGK.LLST..LLSKKLNCYKITLECLPQNVGFYK.FGY..SEENY.C.RFLK
RetrocopyRERVD--VVSSECRGRQLGK-LLSTCSLLSKKLNCYKITLECLPQNVGFYKTFGYIGSEENYICQRFLK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .00 RPM 23 .08 RPM
bodymap2_adrenal 0 .00 RPM 20 .51 RPM
bodymap2_brain 0 .00 RPM 18 .33 RPM
bodymap2_breast 0 .00 RPM 25 .08 RPM
bodymap2_colon 0 .00 RPM 22 .76 RPM
bodymap2_heart 0 .00 RPM 8 .79 RPM
bodymap2_kidney 0 .00 RPM 34 .08 RPM
bodymap2_liver 0 .00 RPM 59 .67 RPM
bodymap2_lung 0 .00 RPM 11 .64 RPM
bodymap2_lymph_node 0 .00 RPM 17 .49 RPM
bodymap2_ovary 0 .00 RPM 33 .35 RPM
bodymap2_prostate 0 .00 RPM 17 .75 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .15 RPM
bodymap2_testis 0 .00 RPM 28 .41 RPM
bodymap2_thyroid 0 .00 RPM 17 .49 RPM
bodymap2_white_blood_cells 0 .00 RPM 13 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4085 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4085 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4085 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4085 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4085 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2770
Gorilla gorilla retro_ggor_2740
Macaca mulatta retro_mmul_2355
Callithrix jacchus retro_cjac_1510
Parental genes homology:
Parental genes homology involve 22 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000034591 retrocopy
retro_chof_2153,
Callithrix jacchus ENSCJAG000000071543 retrocopies
retro_cjac_1479, retro_cjac_1510, retro_cjac_2749,
Dasypus novemcinctus ENSDNOG000000188022 retrocopies
retro_dnov_1564, retro_dnov_548,
Dipodomys ordii ENSDORG000000164141 retrocopy
retro_dord_393,
Homo sapiens ENSG00000100522 3 retrocopies
retro_hsap_2191, retro_hsap_4085 , retro_hsap_4116,
Gorilla gorilla ENSGGOG000000250602 retrocopies
retro_ggor_2740, retro_ggor_2762,
Macropus eugenii ENSMEUG000000030861 retrocopy
retro_meug_930,
Microcebus murinus ENSMICG000000143471 retrocopy
retro_mmur_528,
Macaca mulatta ENSMMUG000000115712 retrocopies
retro_mmul_2355, retro_mmul_2371,
Monodelphis domestica ENSMODG000000145051 retrocopy
retro_mdom_1609,
Mus musculus ENSMUSG000000377221 retrocopy
retro_mmus_1799,
Nomascus leucogenys ENSNLEG000000125102 retrocopies
retro_nleu_321, retro_nleu_583,
Oryctolagus cuniculus ENSOCUG000000078581 retrocopy
retro_ocun_194,
Otolemur garnettii ENSOGAG000000100151 retrocopy
retro_ogar_1704,
Ochotona princeps ENSOPRG000000161369 retrocopies
retro_opri_1142, retro_opri_1221, retro_opri_278, retro_opri_312, retro_opri_544, retro_opri_634, retro_opri_831, retro_opri_940, retro_opri_962,
Pongo abelii ENSPPYG000000058221 retrocopy
retro_pabe_2069,
Pan troglodytes ENSPTRG000000063543 retrocopies
retro_ptro_1667, retro_ptro_2770, retro_ptro_2795,
Rattus norvegicus ENSRNOG000000086411 retrocopy
retro_rnor_2051,
Sarcophilus harrisii ENSSHAG000000054821 retrocopy
retro_shar_379,
Sus scrofa ENSSSCG000000050401 retrocopy
retro_sscr_480,
Tupaia belangeri ENSTBEG000000055382 retrocopies
retro_tbel_4657, retro_tbel_593,
Tursiops truncatus ENSTTRG000000038981 retrocopy
retro_ttru_655,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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