RetrogeneDB ID: retro_hsap_1740

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:28299530..28300044(+)
• Located in intron of: ENSG00000176927

Retrocopy information

• Ensembl ID: ENSG00000264435
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NME4
• Ensembl ID: ENSG00000103202
• Aliases: NME4, NDPK-D, NM23H4, nm23-H4
• Description: NME/NM23 nucleoside diphosphate kinase 4 [Source:HGNC Symbol;Acc:7852]

Sequence

>retro_hsap_1740
CTCTTCAGGCGTGCCACCGCTGCCGGGCCTGCTGTACGACCCGCGGGCTCTGGGCCATGCCTGCTCTTGCGCCCGGCTCA
GGAGGACCCTTCTTGATCCAGGAGTGGACCCTGGTCTCATTGGAGCCAGTTGGGGTCTTGTGGCGGCCTGTTAGGGATGT
GATCCAGCGCTTTGGAGGCAGGGCTTCAAGCTGGTAGGGATGAAGATCCTGTGGCCGGCCAGAAAGCGTCCTTGCTGAAC
ACTACCAGGACCTGCGAAGGAAGCCCCTCTACCCAGCCCTCCTTAGCTATGTGAGCTCCAGGCCTGTTGATGGCCATGGT
CTGGGAAGGGTACAATGTGATCCATGCCTCGAGGGCCATGATAGATACCCTGACAGGGTTGAGGCTGACTCTGTGACCAT
ATGGGGAGACTTCAGCGACGTCCACATCAGCAGGAACATCATTCACACCAGCTATTCAGGGTAGGGGGTCAGAAAGAGAT
CCAGCTGTGGTTTGAAAGCAGTGAGCTGGTGAAC

Alignment

ORF - retro_hsap_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.36 %
• Parental protein coverage: 91.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LFWRSALRGLRCGPRAPGPSLLVRH-GSGGPSWTRERTLVAVKPDGVQRRLVGDVIQRFE-RRGFTLVGM
          LF.R....G....P...GP.LL.R..GSGGP....E.TLV...P.GV..R.V.DVIQRF..R.GF.LVGM
Retrocopy LFRRATAAGPAVRPAGSGPCLLLRP<GSGGPFLIQEWTLVSLEPVGVLWRPVRDVIQRFG<RQGFKLVGM

Parental  KMLQA-PESVLAEHYQDLRRKPFYPALIRYMSSGPV-VAMVWEGYNVVRASRAMIG-HTDSAEAAPGTIR
          K.L...PESVLAEHYQDLRRKP.YPAL..Y.SS.PV..AMVWEGYNV..ASRAMI....D..EA...TI.
Retrocopy KILWP>PESVLAEHYQDLRRKPLYPALLSYVSSRPV>MAMVWEGYNVIHASRAMID<YPDRVEADSVTIW

Parental  GDFS-VHISRNVIHASDS-VEGAQREIQLWFQSSELVS
          GDFS.VHISRN.IH.S.S...G.Q.EIQLWF.SSELV.
Retrocopy GDFSDVHISRNIIHTSYS<RVGGQKEIQLWFESSELVN

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.00 RPM	20.77 RPM
bodymap2_adrenal	0.00 RPM	26.57 RPM
bodymap2_brain	0.00 RPM	8.32 RPM
bodymap2_breast	0.00 RPM	49.20 RPM
bodymap2_colon	0.00 RPM	40.84 RPM
bodymap2_heart	0.00 RPM	17.67 RPM
bodymap2_kidney	0.00 RPM	15.10 RPM
bodymap2_liver	0.00 RPM	39.12 RPM
bodymap2_lung	0.00 RPM	28.59 RPM
bodymap2_lymph_node	0.00 RPM	21.69 RPM
bodymap2_ovary	0.00 RPM	35.32 RPM
bodymap2_prostate	0.00 RPM	91.36 RPM
bodymap2_skeletal_muscle	0.00 RPM	8.46 RPM
bodymap2_testis	0.00 RPM	34.18 RPM
bodymap2_thyroid	0.00 RPM	11.34 RPM
bodymap2_white_blood_cells	0.00 RPM	6.20 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1740 was not detected

EST

No EST(s) were mapped for retro_hsap_1740 retrocopy.

TSS

No TSS is located nearby retro_hsap_1740 retrocopy 5' end.

Lab

retro_hsap_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007077	3 retrocopies	retro_amel_1271, retro_amel_216, retro_amel_238,
Canis familiaris	ENSCAFG00000019677	4 retrocopies	retro_cfam_1267, retro_cfam_2209, retro_cfam_447, retro_cfam_71,
Cavia porcellus	ENSCPOG00000006496	1 retrocopy	retro_cpor_1076,
Echinops telfairi	ENSETEG00000014875	1 retrocopy	retro_etel_1833,
Felis catus	ENSFCAG00000008300	3 retrocopies	retro_fcat_1013, retro_fcat_1512, retro_fcat_1672,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Homo sapiens	ENSG00000103202	1 retrocopy	retro_hsap_1740 ,
Gorilla gorilla	ENSGGOG00000004512	1 retrocopy	retro_ggor_2259,
Macropus eugenii	ENSMEUG00000005455	5 retrocopies	retro_meug_1027, retro_meug_1427, retro_meug_1981, retro_meug_1999, retro_meug_694,
Myotis lucifugus	ENSMLUG00000010061	1 retrocopy	retro_mluc_388,
Macaca mulatta	ENSMMUG00000000612	1 retrocopy	retro_mmul_1221,
Mustela putorius furo	ENSMPUG00000016017	3 retrocopies	retro_mputfur_1024, retro_mputfur_1067, retro_mputfur_846,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Nomascus leucogenys	ENSNLEG00000008068	1 retrocopy	retro_nleu_2719,
Otolemur garnettii	ENSOGAG00000025808	1 retrocopy	retro_ogar_2689,
Pongo abelii	ENSPPYG00000006908	1 retrocopy	retro_pabe_1442,
Pan troglodytes	ENSPTRG00000007541	1 retrocopy	retro_ptro_1220,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sus scrofa	ENSSSCG00000007986	2 retrocopies	retro_sscr_1113, retro_sscr_852,
Ictidomys tridecemlineatus	ENSSTOG00000004798	1 retrocopy	retro_itri_1629,
Tursiops truncatus	ENSTTRG00000009157	2 retrocopies	retro_ttru_393, retro_ttru_688,
Vicugna pacos	ENSVPAG00000010316	1 retrocopy	retro_vpac_150,