RetrogeneDB ID: retro_hsap_1966

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:12670384..12671403(+)
• Located in intron of: ENSG00000269693

Retrocopy information

• Ensembl ID: ENSG00000213290
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGK1
• Ensembl ID: ENSG00000102144
• Aliases: PGK1, HEL-S-68p, MIG10, PGKA
• Description: phosphoglycerate kinase 1 [Source:HGNC Symbol;Acc:8896]

Sequence

>retro_hsap_1966
ATGTCGCTTTCTAACAAGCTGATGCTGGACAAGCTGGACGTGAAAGGGAAGCCGGTCGTTATGAGAGTCGACTTCAATTT
TCCTATGAAGAACAACCAGGTAACAAACAACTGGAGGATTAAGGCTGCTGTCCCAAGCATCAAATTCTGCTTGGACAATG
GATCCAAGTCAGTAGTCCTTATAAGCCACCTAGGTTGGCCTGATGGTGTCCCTATGCCTGACAAGTACTCCTCAGAGCCA
GTTGCTGTAGAACTCAAATCTCTGCTGGGCAAGGATGTTCTGTTCTTGAAGGACTGTGTAGGCCCAGAAGTGGAGAAAGC
CTGTACCAACCCAGCTGCTGGGTCTGTCATCCTGCGGGAGAACCTCCGCTTTCATGTGGAGGAAGAGGGAAGGGAAAAGA
TGCTTCTGGGAACAAGGCTAATGCTGATCCAGCCAAATTAGAAGCTTTCCAAGCTTCACTTCCCAAGCTAGGGGAAGTCT
ATGTCAATGATGCTTTTGGCACTGCTCACAGAGCCCACAGCTCCATGGCAGAAGTCAATCTGCCACAGAAGGCTGGTGGT
TTTTTGATGAAGAAGGAGCTGAACTACTTTGCCGAGGCCTTGGAGAGCCCAGAGCGACCCTTCCTGGCCATCCTGGGCAG
AACTAAAGTTGCAGACAAGATCCAGCTGATCAAGAACATGCTGGGCAAAGTCAATGAGATGATTATTGGTAGTGGAATGG
CTTGTACCTTCCTTAAGGTGCTCAGCAACATGGAGATTGGCACTTCTCTGTTTGATGAAGAGGGAGCCAAGACTGTCAAA
GACCTAATGTCCAAAGCTGAGAAGAATGGTGTGAAGATTATCTTGCCTGTTGACTTTGTCACTGCTGGCAAGTTTGATGA
GAATACCAAGACTGGCCAAGCCACTGTGGCTTCTGGCATACCTGCTGGCTGGCTGGGCTTGGACTGTGGCCCTGAAAGCA
GCAAGAAGTATGCTGGGGCTGTCACTCAGGCTAAGCAGATTGTGTGGAATGGTCCTGTG

Alignment

ORF - retro_hsap_1966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 81.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV
          MSLSNKL.LDKLDVKGK.VVMRVDFN.PMKNNQ.TNN.RIKAAVPSIKFCLDNG.KSVVL.SHLG.PDGV
Retrocopy MSLSNKLMLDKLDVKGKPVVMRVDFNFPMKNNQVTNNWRIKAAVPSIKFCLDNGSKSVVLISHLGWPDGV

Parental  PMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEG-KGKDASGNK
          PMPDKYS.EPVAVELKSLLGKDVLFLKDCVGPEVEKAC.NPAAGSVIL.ENLRFHVEEEG.KGKDASGNK
Retrocopy PMPDKYSSEPVAVELKSLLGKDVLFLKDCVGPEVEKACTNPAAGSVILRENLRFHVEEEG<KGKDASGNK

Parental  VKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFL
          ..A.PAK.EAF.ASL.KLG.VYVNDAFGTAHRAHSSM..VNLPQKAGGFLMKKELNYFA.ALESPERPFL
Retrocopy ANADPAKLEAFQASLPKLGEVYVNDAFGTAHRAHSSMAEVNLPQKAGGFLMKKELNYFAEALESPERPFL

Parental  AILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVK
          AILG..KVADKIQLI.NML.KVNEMIIG.GMA.TFLKVL.NMEIGTSLFDEEGAK.VKDLMSKAEKNGVK
Retrocopy AILGRTKVADKIQLIKNMLGKVNEMIIGSGMACTFLKVLSNMEIGTSLFDEEGAKTVKDLMSKAEKNGVK

Parental  ITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPV
          I.LPVDFVTA.KFDEN.KTGQATVASGIPAGW.GLDCGPESSKKYA.AVT.AKQIVWNGPV
Retrocopy IILPVDFVTAGKFDENTKTGQATVASGIPAGWLGLDCGPESSKKYAGAVTQAKQIVWNGPV

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	0.10 RPM	214.56 RPM
bodymap2_adrenal	0.12 RPM	250.22 RPM
bodymap2_brain	0.05 RPM	392.36 RPM
bodymap2_breast	0.00 RPM	276.09 RPM
bodymap2_colon	0.00 RPM	241.50 RPM
bodymap2_heart	0.04 RPM	339.35 RPM
bodymap2_kidney	0.08 RPM	486.59 RPM
bodymap2_liver	0.00 RPM	195.18 RPM
bodymap2_lung	0.00 RPM	296.64 RPM
bodymap2_lymph_node	0.00 RPM	256.43 RPM
bodymap2_ovary	0.10 RPM	181.49 RPM
bodymap2_prostate	0.16 RPM	228.23 RPM
bodymap2_skeletal_muscle	0.02 RPM	210.82 RPM
bodymap2_testis	0.06 RPM	140.72 RPM
bodymap2_thyroid	0.06 RPM	311.30 RPM
bodymap2_white_blood_cells	0.02 RPM	552.54 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1966 was not detected

EST

No EST(s) were mapped for retro_hsap_1966 retrocopy.

TSS

No TSS is located nearby retro_hsap_1966 retrocopy 5' end.

Lab

retro_hsap_1966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1966 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1429
Pongo abelii	retro_pabe_1624

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017619	1 retrocopy	retro_amel_117,
Bos taurus	ENSBTAG00000000894	1 retrocopy	retro_btau_1021,
Canis familiaris	ENSCAFG00000017270	2 retrocopies	retro_cfam_1194, retro_cfam_510,
Callithrix jacchus	ENSCJAG00000021082	3 retrocopies	retro_cjac_1367, retro_cjac_137, retro_cjac_4171,
Cavia porcellus	ENSCPOG00000023785	1 retrocopy	retro_cpor_102,
Equus caballus	ENSECAG00000014984	1 retrocopy	retro_ecab_557,
Felis catus	ENSFCAG00000013209	2 retrocopies	retro_fcat_123, retro_fcat_316,
Homo sapiens	ENSG00000102144	2 retrocopies	retro_hsap_1966 , retro_hsap_90,
Gorilla gorilla	ENSGGOG00000017111	3 retrocopies	retro_ggor_1429, retro_ggor_2420, retro_ggor_3026,
Loxodonta africana	ENSLAFG00000011954	1 retrocopy	retro_lafr_13,
Macropus eugenii	ENSMEUG00000004779	3 retrocopies	retro_meug_11, retro_meug_1649, retro_meug_400,
Myotis lucifugus	ENSMLUG00000017791	2 retrocopies	retro_mluc_1657, retro_mluc_2159,
Macaca mulatta	ENSMMUG00000012874	1 retrocopy	retro_mmul_144,
Monodelphis domestica	ENSMODG00000004055	2 retrocopies	retro_mdom_140, retro_mdom_170,
Mus musculus	ENSMUSG00000062070	2 retrocopies	retro_mmus_29, retro_mmus_9,
Nomascus leucogenys	ENSNLEG00000001423	3 retrocopies	retro_nleu_2372, retro_nleu_2610, retro_nleu_79,
Oryctolagus cuniculus	ENSOCUG00000014726	1 retrocopy	retro_ocun_171,
Otolemur garnettii	ENSOGAG00000011104	1 retrocopy	retro_ogar_73,
Procavia capensis	ENSPCAG00000002117	1 retrocopy	retro_pcap_17,
Pongo abelii	ENSPPYG00000020496	3 retrocopies	retro_pabe_134, retro_pabe_1624, retro_pabe_3770,
Pan troglodytes	ENSPTRG00000022052	2 retrocopies	retro_ptro_2, retro_ptro_3229,
Rattus norvegicus	ENSRNOG00000002467	7 retrocopies	retro_rnor_1526, retro_rnor_1527, retro_rnor_2603, retro_rnor_3, retro_rnor_462, retro_rnor_590, retro_rnor_611,
Sorex araneus	ENSSARG00000003956	1 retrocopy	retro_sara_14,
Sarcophilus harrisii	ENSSHAG00000001853	1 retrocopy	retro_shar_11,
Sus scrofa	ENSSSCG00000012440	1 retrocopy	retro_sscr_933,
Ictidomys tridecemlineatus	ENSSTOG00000001972	1 retrocopy	retro_itri_65,
Tupaia belangeri	ENSTBEG00000010309	1 retrocopy	retro_tbel_35,
Tarsius syrichta	ENSTSYG00000007917	1 retrocopy	retro_tsyr_40,
Vicugna pacos	ENSVPAG00000001208	1 retrocopy	retro_vpac_21,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.18 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.27 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.18 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.12 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.11 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.13 RPM
GBR_HG00114	0.11 RPM
GBR_HG00119	0.12 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.10 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.19 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.10 RPM
TSI_NA20771	0.31 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.09 RPM
YRI_NA18870	0.10 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.05 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.14 RPM

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Indel association:

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