RetrogeneDB ID: retro_hsap_2904

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:195377630..195378509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000271662
• 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_2904
ATGGACGTCGACAGGCTCCAGGAGGCGCTGGAAGATTTTGAGAAGAGGCAAAAAAGAAAGTCTGTCCTGTCCTGGATCAG
TTCCTTTTGTCATGTAGCCAAGACTGGAGAAACAGATTCCGTGGTCCCAATTTAAAGGCTATTTTATTTTCAAACTGGAG
AAAGTGATGGATGATTTCAGAACTTCAGCTCCTGCGCCAAGAGGTCCTCCCAACCCTAATGTCGAATATATTCCCTGTGA
TGAAACAAAGGGAAGAATACTGAAAAACTGTCACTGGATTTAACCGTATCCCTTTTACTATTCAGCGATTATGTGAATTG
TTAACAGATCCGAGGAGAAACTATACAGGAACAGACAAATTTCTCAGAGGAGTAGAAAAGAACGTGATGGTTGTTAGCTG
TGTTTATCCTTCTTCAGAGAAAAACAATTCCAATAGTTTAAATCGAATGAATGGTGTGATGTTTCCTGGAAATGCACCAA
GCTATACTGAGAGGTCTAATATAAATGGGCCTGGGACACCCAGGCCACGTAATCGACCAAAGGTTTCTCTGTCAGCCCCC
ATGACAACAAATGGGTGGCCTGAGAGCACAGACAGCAAAGAGGCAAATTTGCAGCAAAATGAAGAGAAAACTCAGTGACT
CTTCGACATCTGAATCAGAAGTTTCCTCAGTGAGCCCTTTGAGAAATAAACATCCAGATGAAGATGCTGTGGAAGCTGAG
GGGCATGAGGTAAAAAGACTCAGGTTTGACAAAAAAGGCGAAGTCGGAGAAATAGCCAGTCAAGCGACTTGCAGCGAAAT
TTCTTCAGTTATGGTAGAAGAAACAGAAGCATCACCTTCATCTCATGATAAAGACAAAAAAAGCCATGGTACCCGGCAG

Alignment

ORF - retro_hsap_2904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.9 %
• 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..I.WSQFKGYFIFKLEKVMDDFRTSAP.PR
Retrocopy MDVDRLQEALEDFEKR<AKKKVCPVLDQFLLSCSQDW<EKQIPWSQFKGYFIFKLEKVMDDFRTSAPAPR

Parental  GPPNPNVEYIPFDEMKERILK-IVTGFNGIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYP
          GPPNPNVEYIP.DE.K.RILK..VTGFN.IPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYP
Retrocopy GPPNPNVEYIPCDETKGRILK>TVTGFNRIPFTIQRLCELLTDPRRNYTGTDKFLRGVEKNVMVVSCVYP

Parental  SSEKNNSNSLNRMNGVMFPGNSPSYTERSNINGPGTPRPLNRPKVSLSAPMTTNGLPESTDSKEANLQQN
          SSEKNNSNSLNRMNGVMFPGN.PSYTERSNINGPGTPRP.NRPKVSLSAPMTTNG.PESTDSKEANL.Q.
Retrocopy SSEKNNSNSLNRMNGVMFPGNAPSYTERSNINGPGTPRPRNRPKVSLSAPMTTNGWPESTDSKEANL-QQ

Parental  EEKNH-SDSSTSESEVSSVSPLKNKHPDEDAVEAEGHEVKRLRFDKEGEVRETASQTTSSEISSVMVGET
          .E....SDSSTSESEVSSVSPL.NKHPDEDAVEAEGHEVKRLRFDK.GEV.E.ASQ.T.SEISSVMV.ET
Retrocopy NEEKT>SDSSTSESEVSSVSPLRNKHPDEDAVEAEGHEVKRLRFDKKGEVGEIASQATCSEISSVMVEET

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

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	76.99 RPM
bodymap2_adrenal	0.00 RPM	72.67 RPM
bodymap2_brain	0.19 RPM	89.21 RPM
bodymap2_breast	0.10 RPM	90.37 RPM
bodymap2_colon	0.00 RPM	91.05 RPM
bodymap2_heart	0.02 RPM	95.06 RPM
bodymap2_kidney	0.12 RPM	88.84 RPM
bodymap2_liver	0.00 RPM	52.75 RPM
bodymap2_lung	0.11 RPM	110.44 RPM
bodymap2_lymph_node	0.00 RPM	92.03 RPM
bodymap2_ovary	0.23 RPM	128.06 RPM
bodymap2_prostate	0.00 RPM	67.93 RPM
bodymap2_skeletal_muscle	0.04 RPM	78.92 RPM
bodymap2_testis	0.19 RPM	122.17 RPM
bodymap2_thyroid	0.15 RPM	88.32 RPM
bodymap2_white_blood_cells	0.00 RPM	100.59 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2904 was not detected

EST

No EST(s) were mapped for retro_hsap_2904 retrocopy.

TSS

No TSS is located nearby retro_hsap_2904 retrocopy 5' end.

Lab

retro_hsap_2904 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2904 has 0 orthologous retrocopies within eutheria group .

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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,