RetrogeneDB ID: retro_mmul_1794

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:132709015..132710001(+)
• Located in intron of: ENSMMUG00000000577

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPF2
• Ensembl ID: ENSMMUG00000012317
• Aliases: None
• Description: D4, zinc and double PHD fingers family 2 [Source:HGNC Symbol;Acc:9964]

Sequence

>retro_mmul_1794
AAAAGTGACCGGGTTCTAGGATTGGCCTCTGGACAGCCATACTCTTACCCTGCCCAGCGCTGGCAGAAAAAGCAGCGAGT
CCACCCCCCTGAAGATCCACAAGTTTCCTTCCCATCTGTCAAGCCAGACACAGACCAGACCCTGAAGAAGGAGGGGCTGA
TCTCTCAGGATGGCAGCAGTTTAGAGGTTCTGTTGCACACTGACCCCCTGGAGAAGCGAGGTGCCCCAGGTCCCCGAGTT
GATGATGACAGCCTGGGTGAGTTTCCTGTGACCAACAGTCAAGCACGAAAGCGAATCCTAGAACCAGATGACTTCAATGA
TGAGGACTATGAAGAAGATGCTCCCAAGCATACGGGAAAGGGGTAATCCAAGAGTAAAGGTGTGGGCAGTGCCTGTAAGG
AGCTGGATGCTTCCAACCTGGAGGACCGGGACAAGCCCTATGCCTGTGACATTTGTGGAAAACATTATAAGAACCAACCA
GGCCTCAGCTACCACTATGTCCACTCTCACTTGGCTGAGGAGGAGGGTGAGGACAAAGAAGACTCCCAACCACCCACCCC
TGTTTCCCAGAGGTCTGAGGAACAGAAACCCAAAAAGGGTCCTGATGGATTGGCCTTGCCCAACAACTATTGTAACTTCT
GTCTGGGGAACTCAAAGATTAACAAGAAGATGGGACAACTCGAGGAGCTGGTGTCTTGTTTTGACTGTGGCTGCTCAGGG
CATCCATCTTGCCTCCTTTTCACCCCCATGACGACGGCGGCAGTGAAGACATGCTGCTGGCAGTGCATCGAGTGCGAATG
TCGCGACACCTGCGGCACCGCTGAGAATGATGACCAGCTGGGCTTCCGTGCTGACTGCGATCACGGCTACCAACTGCACT
GTCTCACCTCATCCATGTCTGAGCCCCCGAAGGAAGTGGGAGTTGCCACCTGTGTCTGGACCTGTTGAAGGAGAAAGTTG
CCATCTACCAGAACCAGAACTCCTCT

Alignment

ORF - retro_mmul_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.64 %
• Parental protein coverage: 85.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRHRGPGLASGQLYSYPARRWRKKRRAHPPEDPRLSFPSIKPDTDQTLKKEGLISQDGSSLEALLRTDPL
          K..R..GLASGQ.YSYPA.RW.KK.R.HPPEDP..SFPS.KPDTDQTLKKEGLISQDGSSLE.LL.TDPL
Retrocopy KSDRVLGLASGQPYSYPAQRWQKKQRVHPPEDPQVSFPSVKPDTDQTLKKEGLISQDGSSLEVLLHTDPL

Parental  EKRGAPDPRVDDDSLGEFPVTNSRARKRILEPDDFLDDLDDEDYEEDTPKRRGKGKSKGKGVGSARKKLD
          EKRGAP.PRVDDDSLGEFPVTNS.ARKRILEPDDF.....DEDYEED.PK..GKG.SK.KGVGSA.K.LD
Retrocopy EKRGAPGPRVDDDSLGEFPVTNSQARKRILEPDDF----NDEDYEEDAPKHTGKG*SKSKGVGSACKELD

Parental  ASILEDRDKPYACDICGKRYKTRPGLSYHYAQN--AEEEGEDKEDSQPPTPVSQRSEEQKSKKGPDGLAL
          AS.LEDRDKPYACDICGK.YK..PGLSYHY.....AEEEGEDKEDSQPPTPVSQRSEEQK.KKGPDGLAL
Retrocopy ASNLEDRDKPYACDICGKHYKNQPGLSYHYVHSHLAEEEGEDKEDSQPPTPVSQRSEEQKPKKGPDGLAL

Parental  PNNYCDFCLGDSKINKKTGQPEELVSCSDCGRSGHPSCLQFTPVMMAAVKTYRWQCIECKCCNICGTSEN
          PNNYC.FCLG.SKINKK.GQ.EELVSC.DCG.SGHPSCL.FTP...AAVKT..WQCIEC.C...CGT.EN
Retrocopy PNNYCNFCLGNSKINKKMGQLEELVSCFDCGCSGHPSCLLFTPMTTAAVKTCCWQCIECECRDTCGTAEN

Parental  DDQLLFCDDCDRGYHMYCLTPSMSEP-PEGNWSCHLCLDLLKEKASIYQNQNSS
          DDQL.F..DCD.GY...CLT.SMSEP.PEG..SCHLCLDLLKEK..IYQNQNSS
Retrocopy DDQLGFRADCDHGYQLHCLTSSMSEP<PEGSGSCHLCLDLLKEKVAIYQNQNSS

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	0.00 RPM	15.35 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	24.35 RPM
SRP007412_cerebellum	0.06 RPM	19.18 RPM
SRP007412_heart	0.12 RPM	20.85 RPM
SRP007412_kidney	0.00 RPM	15.49 RPM
SRP007412_liver	0.04 RPM	13.97 RPM
SRP007412_testis	0.08 RPM	61.78 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1794 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1794 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000023858	1 retrocopy	retro_fcat_1341,
Homo sapiens	ENSG00000133884	1 retrocopy	retro_hsap_3660,
Macaca mulatta	ENSMMUG00000012317	1 retrocopy	retro_mmul_1794 ,
Nomascus leucogenys	ENSNLEG00000005574	1 retrocopy	retro_nleu_516,
Tarsius syrichta	ENSTSYG00000000038	1 retrocopy	retro_tsyr_1932,