RetrogeneDB ID: retro_hsap_2744

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:195664113..195664991(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231443
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP4R2
• Ensembl ID: ENSG00000163605
• Aliases: PPP4R2, PP4R2
• Description: protein phosphatase 4, regulatory subunit 2 [Source:HGNC Symbol;Acc:18296]

Sequence

>retro_hsap_2744
ATGGACGTCGACAGGCTCCAGGAGGCGCTGGAAGATTTTGAGAAGAGGCAAAAAAGAAAGTCTGTCCTGTCCTGGATCAG
TTCCTTTTGTCATGTAGCCAAGACTGGAGAAACAGATTCAGTGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAG
AAAGTGATGGATGATTTCAGAACTTCAGCTCCTGCGCCAAGAGGTCCTCCCAACCCTAAAGTCGAATATATTCCCTTTGA
TGAAACAAAGGGAAGAATACTGAAAACTGTCACTGGATTTAACCGTATCCCTTTTACTATTCAGCGATTATGTGAATTGT
TAACAGATCCAAGGAGAAACTATACAGGAACAGACAAATTTCTCAGAGGAGTAGAAAAGAACGTGATGGTTGTTAGCTGT
GTTTATCCTTCTTCAGAGAAAAACAATTCCAATAGTTTAAATCGAATGAATGGTGTGATGTTTCCTGGAAATGCACCAAG
CTATACTGAGAGGTCTAATATAAATGGGCCTGGGACACCCAGGCCACGTAATCGACCAAAGGTTTCTCTGTCAGCCCCAT
GACAACAAATGGGTGGCCTGAGAGCACAGACAGCAAAGAGGCAAATTTGCAGCAAAATGAAGAGAAAACTCACAGTGACT
CTTCGACATCTGAATCAGAAGTTTCCTCAGTGAGCCCTTTGAGAAATAAACATCCAGATGAAGATGCTGTGGAAGCTGAG
GGGTATGAGGTAAAAAGACTCAGGTTTGACAAAAAGGCGAAGTCGGAGAAACAGCCAGTCAAGAGACTTGCAGCGAAATT
TCTTCAGTTATGGTAGAAGAAACAGAAGCATCACCTTCATCTCATGATAAAGACAAAGAAAGCTGTGGTACCCGGCAG

Alignment

ORF - retro_hsap_2744 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.91 %
• Parental protein coverage: 70.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDVERLQEALKDFEKR-GKKEVCPVLDQFLCHVAKTG-ETMIQWSQFKGYFIFKLEKVMDDFRTSAPEPR
          MDV.RLQEAL.DFEKR..KK.VCPVLDQFL........E..IQWSQFKGYFIFKLEKVMDDFRTSAP.PR
Retrocopy MDVDRLQEALEDFEKR<AKKKVCPVLDQFLLSCSQDW<EKQIQWSQFKGYFIFKLEKVMDDFRTSAPAPR

Parental  GPPNPNVEYIPFDEMKERILKIVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPS
          GPPNP.VEYIPFDE.K.RILK.VTGFN.IPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPS
Retrocopy GPPNPKVEYIPFDETKGRILKTVTGFNRIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYPS

Parental  SEKNNSNSLNRMNGVMFPGNSPSYTERSNINGPGTPRPLNRPKVSLSAP-MTTNGLPESTDSKEANLQQN
          SEKNNSNSLNRMNGVMFPGN.PSYTERSNINGPGTPRP.NRPKVSLSAP.MTTNG.PESTDSKEANLQQN
Retrocopy SEKNNSNSLNRMNGVMFPGNAPSYTERSNINGPGTPRPRNRPKVSLSAP<MTTNGWPESTDSKEANLQQN

Parental  EEKNHSDSSTSESEVSSVSPLKNKHPDEDAVEAEGHEVKRLRFDK-EGEVRETASQTTSSEISSVMVGET
          EEK.HSDSSTSESEVSSVSPL.NKHPDEDAVEAEG.EVKRLRFDK..GEV.ETASQ.T.SEISSVMV.ET
Retrocopy EEKTHSDSSTSESEVSSVSPLRNKHPDEDAVEAEGYEVKRLRFDK<KGEVGETASQETCSEISSVMVEET

Parental  EASSSSQDKDKDSRCTRQ
          EAS.SS.DKDK.S..TRQ
Retrocopy EASPSSHDKDKESCGTRQ

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	0.08 RPM	76.99 RPM
bodymap2_adrenal	0.27 RPM	72.67 RPM
bodymap2_brain	0.14 RPM	89.21 RPM
bodymap2_breast	0.12 RPM	90.37 RPM
bodymap2_colon	0.00 RPM	91.05 RPM
bodymap2_heart	0.18 RPM	95.06 RPM
bodymap2_kidney	0.39 RPM	88.84 RPM
bodymap2_liver	0.00 RPM	52.75 RPM
bodymap2_lung	0.00 RPM	110.44 RPM
bodymap2_lymph_node	0.00 RPM	92.03 RPM
bodymap2_ovary	0.13 RPM	128.06 RPM
bodymap2_prostate	0.03 RPM	67.93 RPM
bodymap2_skeletal_muscle	0.02 RPM	78.92 RPM
bodymap2_testis	0.09 RPM	122.17 RPM
bodymap2_thyroid	0.02 RPM	88.32 RPM
bodymap2_white_blood_cells	0.00 RPM	100.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2744 was not detected

EST

No EST(s) were mapped for retro_hsap_2744 retrocopy.

TSS

No TSS is located nearby retro_hsap_2744 retrocopy 5' end.

Lab

retro_hsap_2744 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2744 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1855

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007954	3 retrocopies	retro_chof_1347, retro_chof_1914, retro_chof_2285,
Echinops telfairi	ENSETEG00000019946	2 retrocopies	retro_etel_1238, retro_etel_148,
Homo sapiens	ENSG00000163605	6 retrocopies	retro_hsap_2744 , retro_hsap_2745, retro_hsap_2746, retro_hsap_2904, retro_hsap_3138, retro_hsap_3283,
Loxodonta africana	ENSLAFG00000000513	1 retrocopy	retro_lafr_603,
Macaca mulatta	ENSMMUG00000016959	1 retrocopy	retro_mmul_1224,
Mus musculus	ENSMUSG00000052144	3 retrocopies	retro_mmus_1068, retro_mmus_1157, retro_mmus_3474,
Oryctolagus cuniculus	ENSOCUG00000006235	1 retrocopy	retro_ocun_292,
Pan troglodytes	ENSPTRG00000015108	5 retrocopies	retro_ptro_1855, retro_ptro_1856, retro_ptro_2121, retro_ptro_2220, retro_ptro_2974,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.28 RPM
CEU_NA11843	0.54 RPM
CEU_NA11930	0.65 RPM
CEU_NA12004	0.11 RPM
CEU_NA12400	0.32 RPM
CEU_NA12751	0.68 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.66 RPM
CEU_NA12872	0.60 RPM
CEU_NA12873	0.89 RPM
FIN_HG00183	0.96 RPM
FIN_HG00277	0.26 RPM
FIN_HG00315	0.30 RPM
FIN_HG00321	0.36 RPM
FIN_HG00328	0.36 RPM
FIN_HG00338	0.26 RPM
FIN_HG00349	0.14 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.20 RPM
FIN_HG00378	0.13 RPM
GBR_HG00099	0.20 RPM
GBR_HG00111	0.37 RPM
GBR_HG00114	0.42 RPM
GBR_HG00119	0.98 RPM
GBR_HG00131	0.63 RPM
GBR_HG00133	0.58 RPM
GBR_HG00134	0.72 RPM
GBR_HG00137	0.96 RPM
GBR_HG00142	0.56 RPM
GBR_HG00143	0.38 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.63 RPM
TSI_NA20518	0.39 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.29 RPM
TSI_NA20765	0.44 RPM
TSI_NA20771	0.20 RPM
TSI_NA20786	0.10 RPM
TSI_NA20798	0.37 RPM
YRI_NA18870	0.44 RPM
YRI_NA18907	0.07 RPM
YRI_NA18916	0.38 RPM
YRI_NA19093	0.29 RPM
YRI_NA19099	0.45 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.45 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.52 RPM

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Indel association:

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