RetrogeneDB ID: retro_hsap_380

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:48790966..48791795(-)
• Located in intron of: ENSG00000132122

Retrocopy information

• Ensembl ID: ENSG00000224986
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1R8
• Ensembl ID: ENSG00000117751
• Aliases: PPP1R8, ARD-1, ARD1, NIPP-1, NIPP1, PRO2047
• Description: protein phosphatase 1, regulatory subunit 8 [Source:HGNC Symbol;Acc:9296]

Sequence

>retro_hsap_380
ATGGTGGCAGTCACAGACTCTGGCTCCAGCCTCCCGCTGCTCCACTGCCCAACCTGGGCAGGTAAGCCCCCTTCTGGTTG
ACATCTGGATTTAGTTAAACGAGACAAACTAATTGAGAAACTGATTATTGGTGAAAAGAAGTATTACTTATTTGGGATAA
ACCTTGATTTGTGTGACTTTACCACTGAACACCAGTCTTGCTCTTGGATCCATACTGCACTTGCCTACCACAAGCATCTG
AGGAGAGTTTTCCTGATAGATCTCAACAGTACACACAGCACTTTCTTGGTCACATTCAGTTGGAGCCTCACAAGCCTCAG
CAAATTCCGACTGATTCCAGGGTCTCATTTGACGCATCCACAGGGGCATACACCTTGCGCGAGATACTTGGGCCATTGCC
ATTGGCTCTGAAAGGAATTGAGAAGACGGGTGAAGAGGATGATTAACTCAGGGGCTTACTGGGGCTTCCAGAGGAGGAAA
CTAAGCTTGATAACCTGACATAGTTCAACACTGCCCACAACAAGTGGATTTCCACCTTTACCATTGAGGAGGGAAATCTA
ACATTCCAAGACCAAAGAGGAAGAGGAAGAACTCCCGGGTGACATTCAGTGAGGATGATGAGATCATCAACTCAGAGAAT
GTGGATCCCTCAGTTTGTCGATTCAGGAACATAGTGCAAACTGCAGTGGTCCCAGTCAAGAAGAAGCTGGGGGAGGGCCC
TGGCTCCTTGGGCCTGGAGGAATCAGGGAGAAGGCGCATGCAGAACTTTGCCTTCAGGGGAGGACTCTACGGGGGCCTGT
GCCCTACACACAGTGAAGCAGGCTCCCAG

Alignment

ORF - retro_hsap_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 78.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAANSGSSLPLFDCPTWAGKPPPGLHLDVVKGDKLIEKLIIDEKKYYLFGRNPDLCDFTIDHQSCSRV
          M.A...SGSSLPL..CPTWAGKPP.G.HLD.VK.DKLIEKLII.EKKYYLFG.N.DLCDFT..HQSCS..
Retrocopy MVAVTDSGSSLPLLHCPTWAGKPPSG*HLDLVKRDKLIEKLIIGEKKYYLFGINLDLCDFTTEHQSCSWI

Parental  HAALVYHKHLKRVFLIDLNSTHGT-FLGHIRLEPHKPQQIPIDSTVSFGASTRAYTLREKPQTLPSAVKG
          H.AL.YHKHL.RVFLIDLNSTH.T.FLGHI.LEPHKPQQIP.DS.VSF.AST.AYTLRE....LP.A.KG
Retrocopy HTALAYHKHLRRVFLIDLNSTHST<FLGHIQLEPHKPQQIPTDSRVSFDASTGAYTLREILGPLPLALKG

Parental  DEKMGGEDDELKGLLGLPEEETELDNLTEFNTAHNKRISTLTIEEGNL-DIQRPKRKRKNSRVTFSEDDE
          .EK.G.EDD.L.GLLGLPEEET.LDNLT.FNTAHNK.IST.TIEEGNL..I.RPKRKRKNSRVTFSEDDE
Retrocopy IEKTGEEDD*LRGLLGLPEEETKLDNLT*FNTAHNKWISTFTIEEGNL<NIPRPKRKRKNSRVTFSEDDE

Parental  IINPEDVDPSVGRFRNMVQTAVVPVKKKRVEGPGSLGLEESGSRRMQNFAFSGGLYGGLPPTHSEAGSQ
          IIN.E.VDPSV.RFRN.VQTAVVPVKKK..EGPGSLGLEESG.RRMQNFAF.GGLYGGL.PTHSEAGSQ
Retrocopy IINSENVDPSVCRFRNIVQTAVVPVKKKLGEGPGSLGLEESGRRRMQNFAFRGGLYGGLCPTHSEAGSQ

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	0.02 RPM	27.09 RPM
bodymap2_adrenal	0.06 RPM	41.33 RPM
bodymap2_brain	0.00 RPM	33.92 RPM
bodymap2_breast	0.02 RPM	30.86 RPM
bodymap2_colon	0.00 RPM	28.17 RPM
bodymap2_heart	0.06 RPM	16.47 RPM
bodymap2_kidney	0.00 RPM	29.04 RPM
bodymap2_liver	0.00 RPM	15.99 RPM
bodymap2_lung	0.11 RPM	13.92 RPM
bodymap2_lymph_node	0.00 RPM	27.30 RPM
bodymap2_ovary	0.08 RPM	50.99 RPM
bodymap2_prostate	0.02 RPM	41.36 RPM
bodymap2_skeletal_muscle	0.00 RPM	16.71 RPM
bodymap2_testis	0.36 RPM	50.34 RPM
bodymap2_thyroid	0.02 RPM	44.57 RPM
bodymap2_white_blood_cells	0.00 RPM	48.39 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_380 was not detected

EST

No EST(s) were mapped for retro_hsap_380 retrocopy.

TSS

No TSS is located nearby retro_hsap_380 retrocopy 5' end.

Lab

retro_hsap_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_380 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_296
Macaca mulatta	retro_mmul_491

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012023	1 retrocopy	retro_cfam_334,
Homo sapiens	ENSG00000117751	1 retrocopy	retro_hsap_380 ,
Gorilla gorilla	ENSGGOG00000012062	1 retrocopy	retro_ggor_387,
Loxodonta africana	ENSLAFG00000017834	1 retrocopy	retro_lafr_1173,
Macaca mulatta	ENSMMUG00000006933	1 retrocopy	retro_mmul_491,
Pan troglodytes	ENSPTRG00000000417	1 retrocopy	retro_ptro_296,
Ictidomys tridecemlineatus	ENSSTOG00000004381	2 retrocopies	retro_itri_1611, retro_itri_1704,

Population studies

Expression level across human populations :

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	0.04 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	0.03 RPM
FIN_HG00375	0.02 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	0.02 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

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Indel association:

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