RetrogeneDB ID: retro_hsap_4850

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:67290364..67291225(-)
• Located in intron of: ENSG00000079482

Retrocopy information

• Ensembl ID: ENSG00000228328
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGK1
• Ensembl ID: ENSG00000269666
• Aliases: None
• Description: phosphoglycerate kinase 1 [Source:HGNC Symbol;Acc:8896]

Sequence

>retro_hsap_4850
AAGGGAAGGGAAAACTCTGGGAACAAGGTTAAAGTGAGCCCGCCAAAATAGAAGCTTTCCGAGCTTCACTTTCCAAGCTA
GGGAATGTGCATGTCAATGGTGCTTTTGGCACTGCTCACAGAGCCCACAGCTCCATGGTAGGAGTCAGTCTGCCACAGAA
GGCTGGTGGTTTTTTGATGAAGAAGGAGCTGAACTACTTTGTGAAGGTCTTGGAGAGCCCATAGCGACCCTTCCTGGCCA
TTCTGGGTGGAGCTAAATTTGCAGACAAGATCCACCTGATCAATAATATGCTGGACAAAGTCAATGAGATGATTATTGGT
GGTGGAACGGCTTTTACCTTCCTTAAGGTGCTCAACAACATGGAGACTGGCACTTCTCTGTTTGATGAAGAGGGAGCCAA
GATTGTCAAAGACCTAATGTCCCAAGCTGAGAAGAATGGTGTGAAGATTACCTTGCCTATTGACTTTGTCACTGCTGAGA
AATTTGATGAGAATGCCAAGACTGGCCAAGCCACTGTGGCTTCTGGCATACCTGCTGGCTGAATGGGCTTGGACTGTGGT
CCTGAAAGCAGCAAGAAGTATGCTGAGACTGTCACTTGGGCTAAGCAGATTGTGTGGAATGGTCCTGTGGGGGGTATTTG
AATGGGAAGCTTTTGCCCAGGGAACCAAAGCCCTCATGGATGAGGTGGTGAAAGCCACTTCTAGGGGCTGCATTACCATC
ATAGGTGGTGGAAACACTGCCACTTGCTGTGCCAAATGGAACACAGAGGATAAAATCAGACATGTGAGCACTACGGGTGG
TGCCAGTTTAGAGCTCCTGGACAGTAAAGTCCTTCCTGGGGTGGATGCTCTCGGCAATATT

Alignment

ORF - retro_hsap_4850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.27 %
• Parental protein coverage: 68.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGKDASGNKVK-AEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAK
          KG...SGNKVK..EPAKIEAFRASLSKLG.V.VN.AFGTAHRAHSSMVGV.LPQKAGGFLMKKELNYF.K
Retrocopy KGRENSGNKVK<SEPAKIEAFRASLSKLGNVHVNGAFGTAHRAHSSMVGVSLPQKAGGFLMKKELNYFVK

Parental  ALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDL
          .LESP.RPFLAILGGAK.ADKI.LINNMLDKVNEMIIGGG.AFTFLKVLNNME.GTSLFDEEGAKIVKDL
Retrocopy VLESP*RPFLAILGGAKFADKIHLINNMLDKVNEMIIGGGTAFTFLKVLNNMETGTSLFDEEGAKIVKDL

Parental  MSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGP
          MS.AEKNGVKITLP.DFVTA.KFDENAKTGQATVASGIPAG.MGLDCGPESSKKYAE.VT.AKQIVWNGP
Retrocopy MSQAEKNGVKITLPIDFVTAEKFDENAKTGQATVASGIPAG*MGLDCGPESSKKYAETVTWAKQIVWNGP

Parental  V-GVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVL
          V.GVFEWEAFA.GTKALMDEVVKATSRGCITIIGGG.TATCCAKWNTEDK..HVST.GGASLELL..KVL
Retrocopy V>GVFEWEAFAQGTKALMDEVVKATSRGCITIIGGGNTATCCAKWNTEDKIRHVSTTGGASLELLDSKVL

Parental  PGVDALSNI
          PGVDAL.NI
Retrocopy PGVDALGNI

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	0.04 RPM	0.00 RPM
bodymap2_adrenal	0.10 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.00 RPM
bodymap2_breast	0.00 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.00 RPM	0.00 RPM
bodymap2_prostate	0.07 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.06 RPM	0.00 RPM
bodymap2_thyroid	0.00 RPM	0.00 RPM
bodymap2_white_blood_cells	0.04 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4850 was not detected

EST

No EST(s) were mapped for retro_hsap_4850 retrocopy.

TSS

No TSS is located nearby retro_hsap_4850 retrocopy 5' end.

Lab

retro_hsap_4850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4850 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3229
Gorilla gorilla	retro_ggor_3026
Pongo abelii	retro_pabe_3770

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000269666	1 retrocopy	retro_hsap_4850 ,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.11 RPM
CEU_NA11843	0.26 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.23 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.05 RPM
CEU_NA12760	0.13 RPM
CEU_NA12827	0.24 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.22 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.24 RPM
FIN_HG00328	0.17 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.14 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.17 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.25 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.19 RPM
TSI_NA20532	0.14 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.14 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.10 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.08 RPM

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Indel association:

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