RetrogeneDB ID: retro_hsap_474

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:173332108..173332878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000231615
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CEP57
• Ensembl ID: ENSG00000166037
• Aliases: CEP57, MVA2, PIG8, TSP57
• Description: centrosomal protein 57kDa [Source:HGNC Symbol;Acc:30794]

Sequence

>retro_hsap_474
GCGTTGGTCTCTGCTGCTTCTGGTTCTCAGTTCTCAAACATCTTAACTGAACCATCAGGGCCTTAGGGAAGCCTGTTCAG
CATTCTTCATCTCCAAATGTAGTACATCCATCCGATAAGCCTTTCCTTAAGAGTGATCTACGACACTCCCCAAATAAGCC
TACACTTGCCTATCCAGAAAGCAACAGCAGAGCTATATTTTGTGCTCTTAAGAATCTTAAAGGTAAGATTTGATGCTTGG
AACTTGAAATGATTCTGGCAGAAGAAAGTGTGAAAACCTTGTCTAGAGAAACAATTGAATCCAAGAAGGTACTGGATGGA
GAGATATGGGAAAGGGAGAATTCAAAGAATGAAGAATCAAAGCACAATCAAGAACTGATATCTCAGTTGATAGCTGCAGA
AAATAAATGTAATCTTTTAGGAAAACAATTGGAATACATGTGAAATATGATAAAGCATGCAGAAAGGGAGAGGACATCTG
TCTTAGAGAAACAGGTTTCCCTAGAAAGAGAATGGCGATACAATCAAAGACATGTTTGGAGCCAACTTGAAAAATTGGAT
CTTTATGAATGGGAGTATAACTTTCCACAGTGCAGGCCCTTGCAGAAAGAAAAATGTAAGAGTTGGTAGCAAAACTCTGA
AGAAGAACAGGAAAGGAAACATGTACAAACTAAGGCAGCTAAGTTACAGACTGGTCTAGAAACAAATAGACTTATTATTG
AAGATAAGGCAAGTCCGCATTTTCCCAGTGCAAGAAGAATTTTAAAAAAA

Alignment

ORF - retro_hsap_474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.69 %
• Parental protein coverage: 51.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASVSAASGSHLSNSFAEPS-RSNGSMVRHSSSPYVVYPSDKPFLNSDLRRSPSKPTLAYPESNSRAIFSA
          A.VSAASGS..SN...EPS.R..G..V.HSSSP.VV.PSDKPFL.SDLR.SP.KPTLAYPESNSRAIF.A
Retrocopy ALVSAASGSQFSNILTEPS<RALGKPVQHSSSPNVVHPSDKPFLKSDLRHSPNKPTLAYPESNSRAIFCA

Parental  LKNLQDKIRRLELERIQAEESVKTLSRETIEYKKVLDEQIQERENSKNEESKHNQELTSQLLAAENKCNL
          LKNL..KI..LELE.I.AEESVKTLSRETIE.KKVLD..I.ERENSKNEESKHNQEL.SQL.AAENKCNL
Retrocopy LKNLKGKI*CLELEMILAEESVKTLSRETIESKKVLDGEIWERENSKNEESKHNQELISQLIAAENKCNL

Parental  LEKQLEYMRNMIKHAEMERTSVLEKQVSLERERQHDQTHVQSQLEKLDLLEQEYNKLTTMQALAEKKMQE
          L.KQLEYM.NMIKHAE.ERTSVLEKQVSLERE....Q.HV.SQLEKLDL.E.EYN.......L...K...
Retrocopy LGKQLEYM*NMIKHAERERTSVLEKQVSLEREWRYNQRHVWSQLEKLDLYEWEYN-FPQCRPLQKEKCKS

Parental  LEAKLHEEEQERKRMQAKAAELQTGLETNRLIFEDKATPCVPNARRIKKK
          ......EE.QERK..Q.KAA.LQTGLETNRLI.EDKA.P..P.ARRI.KK
Retrocopy W*QNSEEE-QERKHVQTKAAKLQTGLETNRLIIEDKASPHFPSARRILKK

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	37.59 RPM
bodymap2_adrenal	0.00 RPM	45.87 RPM
bodymap2_brain	0.00 RPM	41.70 RPM
bodymap2_breast	0.14 RPM	38.37 RPM
bodymap2_colon	0.00 RPM	55.09 RPM
bodymap2_heart	0.00 RPM	21.34 RPM
bodymap2_kidney	0.00 RPM	41.71 RPM
bodymap2_liver	0.00 RPM	44.91 RPM
bodymap2_lung	0.00 RPM	40.05 RPM
bodymap2_lymph_node	0.00 RPM	44.77 RPM
bodymap2_ovary	0.00 RPM	63.19 RPM
bodymap2_prostate	0.00 RPM	57.49 RPM
bodymap2_skeletal_muscle	0.00 RPM	13.50 RPM
bodymap2_testis	0.06 RPM	77.92 RPM
bodymap2_thyroid	0.00 RPM	59.51 RPM
bodymap2_white_blood_cells	0.00 RPM	64.01 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_474 was not detected

EST

No EST(s) were mapped for retro_hsap_474 retrocopy.

TSS

No TSS is located nearby retro_hsap_474 retrocopy 5' end.

Lab

retro_hsap_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_474 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000000996	1 retrocopy	retro_etel_1557,
Homo sapiens	ENSG00000166037	1 retrocopy	retro_hsap_474 ,
Homo sapiens	ENSG00000183137	1 retrocopy	retro_hsap_591,
Macaca mulatta	ENSMMUG00000014796	1 retrocopy	retro_mmul_575,
Nomascus leucogenys	ENSNLEG00000007130	1 retrocopy	retro_nleu_888,
Tupaia belangeri	ENSTBEG00000003141	1 retrocopy	retro_tbel_2135,