RetrogeneDB ID: retro_ptro_1807

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:101782568..101784227(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: WWP1
• Ensembl ID: ENSPTRG00000020395
• Aliases: None
• Description: E3 ubiquitin-protein ligase [Source:UniProtKB/TrEMBL;Acc:H2QWD9]

Sequence

>retro_ptro_1807
ATGGCCACTGCCTCACCAAAGTCTGATACTACTAATAACCACAGTGGAAGGTTGCAGTTACAGGTAACTGTTTCTAGTGC
CAAACTTAAGAGAAGAAAGAACTGGTTCGGAACAGCAATATATACAGAAGTAGTTGTAGATGAAGAAATTAGGAAAACAG
CAAAATCCAGTAGTTCTTCTAATCCAAAATGGGATGAAGAGCTAACTGTAAATGTTACGCCACAGACTACATTGGAATTT
CGAGTTTGGAGTCATCACACTTTAAAAGCAGATGCTTAATTAGGAAATGCAACGACAGATCTGAAACAAGCTCTGTTGAT
ACACAATAGAAAACTGGAAAGAGTGAAAGAACAATTAAAACTTTCCTTAGAAAACAAGAATGGCATAGCACAAACTGGTG
AATTGACAGTTGTGCTTGATGGATTGGTGATTGAGCAAGAAAATATAACAAACTGCAGCTCATCTCCAGCCATAGAAATA
CAGCAAAATGGTGATGCCTTACATGAAAATGGAGAGCCTTCAGCAAGGACAACTGCCAGGTTGGCTATTGAAGGTACGAA
TGGAATAGATAATCATGTACCTACAAGCACTCTAGTCCAAAACTCATGCTGCTCATATGTAGTTAATGGAGACAACATAC
CTTCATCTCCATCTCAGGTTGCTGCCAGACCCAAAAATACACCAGCCCCAAAACTACTCACATCTGAGCCTGCCGATGAC
ACTGTTAATGGAGAATCATCCTCATTTGCACCAACTGATAATGCTTCTGTCATGGGTATTCCAGTAGTGTCTGAAGAAAA
TGCCTTGTCTCCAAATTGCACTAGTACTACTGTTGAAGATCCTCCAGTTCAAGAAATACTGACTTCCTCAGAAAACAATG
AATGCATTCCTTCTACCAGTGCAGAATTGGGATCTGAATCTAGAAGTATATTAGACCCTGACACCTCTAATTCTGGAAGT
AGTTCTGCTTTTGAAACAGCCAAATCAAGACAGCCAGATGGGTGTATGGATCCGGTATAGCAGGAGTCTGGGAATGCCAA
CACAGAAACCTTGCCATCAGGGTGGGAACAAAGAAAATATCCTCATGGTAGAACCTATTATGTGGGTCATAATACTCAAA
CTACCACACGGGAGAGACCACAACCTTTACCTTCAGGTTGGGAAAGAAGAGTTGATGATCGTGGAAGAGTTTATTATGTG
GATCATAACACCAGAACAACAACATGGCAGCGGCCTACCATGGAATGGGTCAGAAATTTTGAACAGTGGCAATCTCAGCA
GAACCAACCTCAGGGAGCTATGCAACAGTTTAACCAATGATACCTCTATTCAGCTTAAATGTTAGCTGCAGAAAATGACC
CTCATGGACCTTTGCCACCAGGCCGGGAAAAAAGAGTGGATTCAACAGACAGGGTTTACTTTGCGAATCATAATACAAAA
ACAACCCAGTGGGAAGATCCAAGAACTCAAGGCTTACAGAATGAAGAACCTCTGCCAGAAGGCTGGGAAATTAGATATAC
TCGTGAAGGTGTAAGGTACTTTGTTTATCACAATGCAAGAACAACAACATTCAAAGATCCTTGCAATGGGAAATCATCCA
TAACTAAAAGTGGTCCACAAATTGATTATGAACACAGCTTTAGGCAGAAACTTGCTCAC

Alignment

ORF - retro_ptro_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.79 %
• Parental protein coverage: 59.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATASPRSDTSNNHSGRLQLQVTVSSAKLKRKKNWFGTAIYTEVVVDGEITKTAKSSSSSNPKWDEQLTV
          MATASP.SDT.NNHSGRLQLQVTVSSAKLKR.KNWFGTAIYTEVVVD.EI.KTAKSSSSSNPKWDE.LTV
Retrocopy MATASPKSDTTNNHSGRLQLQVTVSSAKLKRRKNWFGTAIYTEVVVDEEIRKTAKSSSSSNPKWDEELTV

Parental  NVTPQTTLEFQVWSHRTLKADALLGKATIDLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD
          NVTPQTTLEF.VWSH.TLKADA.LG.AT.DLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD
Retrocopy NVTPQTTLEFRVWSHHTLKADA*LGNATTDLKQALLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLD

Parental  GLVIEQENITNCSSSPTIEIQENGDALHENGEPSARTTARLAVEGTNGIDNHIPTSTLVQNSCCSYVVNG
          GLVIEQENITNCSSSP.IEIQ.NGDALHENGEPSARTTARLA.EGTNGIDNH.PTSTLVQNSCCSYVVNG
Retrocopy GLVIEQENITNCSSSPAIEIQQNGDALHENGEPSARTTARLAIEGTNGIDNHVPTSTLVQNSCCSYVVNG

Parental  DNTPSSPSQVAARPKNTPAPKPLASEPADDTVNGESSSFAPTDNASVTGTPVVSEENALSPNCTSTTVED
          DN.PSSPSQVAARPKNTPAPK.L.SEPADDTVNGESSSFAPTDNASV.G.PVVSEENALSPNCTSTTVED
Retrocopy DNIPSSPSQVAARPKNTPAPKLLTSEPADDTVNGESSSFAPTDNASVMGIPVVSEENALSPNCTSTTVED

Parental  PPVQEILTSSENNECIPSTSAELESEARSILEPDTSNSRSSSAFEAAKSRQPDGCMDPVRQQSGNANTET
          PPVQEILTSSENNECIPSTSAEL.SE.RSIL.PDTSNS.SSSAFE.AKSRQPDGCMDPV.Q.SGNANTET
Retrocopy PPVQEILTSSENNECIPSTSAELGSESRSILDPDTSNSGSSSAFETAKSRQPDGCMDPV*QESGNANTET

Parental  LPSGWEQRKDPHGRTYYVDHNTRTTTWERPQPLPPGWERRVDDRRRVYYVDHNTRTTTWQRPTMESVRNF
          LPSGWEQRK.PHGRTYYV.HNT.TTT.ERPQPLP.GWE.............HNTRTTTWQRPTME.VRNF
Retrocopy LPSGWEQRKYPHGRTYYVGHNTQTTTRERPQPLPSGWEXXXXXXXXXXXXXHNTRTTTWQRPTMEWVRNF

Parental  EQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPYGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQ
          EQWQSQ.NQ.QGAMQQFNQ.YLYSA.MLAAENDP.GPLPPG.EKRVDSTDRVYF.NHNTKTTQWEDPRTQ
Retrocopy EQWQSQQNQPQGAMQQFNQ*YLYSA*MLAAENDPHGPLPPGREKRVDSTDRVYFANHNTKTTQWEDPRTQ

Parental  GLQNEEPLPEGWEIRYTREGVRYFVDHNTRTTTFKDPRNGKSSVTKGGPQIAYERGFRWKLAH
          GLQNEEPLPEGWEIRYTREGVRYFV.HN.RTTTFKDP.NGKSS.TK.GPQI.YE..FR.KLAH
Retrocopy GLQNEEPLPEGWEIRYTREGVRYFVYHNARTTTFKDPCNGKSSITKSGPQIDYEHSFRQKLAH

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	24.92 RPM
SRP007412_cerebellum	0.00 RPM	22.73 RPM
SRP007412_heart	0.03 RPM	113.09 RPM
SRP007412_kidney	0.00 RPM	61.64 RPM
SRP007412_liver	0.00 RPM	46.29 RPM
SRP007412_testis	0.11 RPM	54.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1807 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1807 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2680
Pongo abelii	retro_pabe_2299
Macaca mulatta	retro_mmul_1418

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000123124	1 retrocopy	retro_hsap_2680,
Macaca mulatta	ENSMMUG00000006305	1 retrocopy	retro_mmul_1418,
Mustela putorius furo	ENSMPUG00000010807	1 retrocopy	retro_mputfur_963,
Mus musculus	ENSMUSG00000041058	1 retrocopy	retro_mmus_2017,
Nomascus leucogenys	ENSNLEG00000001517	1 retrocopy	retro_nleu_1183,
Pongo abelii	ENSPPYG00000018724	1 retrocopy	retro_pabe_2299,
Pan troglodytes	ENSPTRG00000020395	1 retrocopy	retro_ptro_1807 ,