RetrogeneDB ID: retro_mmul_1689

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:77131424..77132699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC7
• Ensembl ID: ENSMMUG00000011010
• Aliases: None
• Description: cell division cycle 7-related protein kinase [Source:RefSeq peptide;Acc:NP_001253539]

Sequence

>retro_mmul_1689
TCCTTTCAAGAAGTACGGGAATATATGTTTAATCTGTTCAAAGCTTTGAAACGCATCCATCAGTTTGGTATTGTTCACCG
TGATGTTAAGCCCAGCAATTTTTTATATAATAGGCGCTTGAAAAAGTATGCCTTGGTAGACTTTGGTTTGGCCCAAGGAA
CCCATGATATTAAAATAGAGCTTTTCAAATTTGTCCAGTCTGAAGCTCAGCAGGAAAGGTGTTCACAAAACAAATCCCAT
ATAATCACAGGAAACAGGATTCCATTGAGTGGCCCAGTACCTAAGGATCTGGATCAGCAGTCCACCACAAAAGCTTCTGT
TAAAAGACCCTGCACAAAGGCACAAATTCAGATTAAACAAGGAAAAGATGGAAAGGAGGGATCTGTAGGCCTTTCTGTCC
AGCGCTCTGTTTTTGGAAAAAGAAATTTCAATATACACAGCTCCATTTCACATGAGAGCCCTGCAGTGAAACTCATGAAG
CAGTCAAAGACTGTGGATGTACTGTCTAGAAAGTTAGCAACAAAAAAGAAGGTTATTTCTGCAAAAGTTATGAATAGTGG
TGTGATGAGGAAAGCTGCCAGTTCTTGCCCGGCTAGCCTGACCTGTGACTGCTATGCAACAGATAAAGTTTGTAGTATTT
GCCCTTCAAGGCGTCAGCAGGTTGCCCCTAGGGCAGGTACACCAGGATTCAGAGCACCAGAGGTCTTGACAAAGTGCCCC
AATCAAACTACAGCAATTGACATGTGGTCTGCAGGTGTCATATTTCTTTCTTTGCTTAGTGGACGATACCCATTTTATAA
AGCAAGTGATGATTTAACTGCTTTGGCCCAAATTATGACAATTCAGGGATCCAGAGAAACTATGCAAGCTGCTAAAACTT
TTGGGAAATCAATATTATGTAGCAAAGAAGTTCCAGCACAAGACTTGAGAAAACTCTGTGAGAGACTCAGGGGTATGGAT
TCCAACACTCCCAAGTAAACAAGTGATATACAAGGGCCTACTTCTCATCAACCAACTATTTCAGAGAAGACTGACCATAA
AGCTTCTCGCCTCGTACAAACACCTCCAGGACAATACTCAGGGAATTCATTTAAAAAGGGGGATAGTAATAGCTGTGGGT
GTTGTTTTGATGAGTATACTACCAATTTAGAAGGCTGGAATGAGGTACCTGATGAAGCTTATGACCTACTTGATAAACTG
CTAGATCTAAATCCAGCTTCAAGAATAACAGCAGAAGAAGTTTTGTTGCATCCATTTTTTAAAGATATGAGCTTG

Alignment

ORF - retro_mmul_1689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.76 %
• Parental protein coverage: 74.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFQEVREYMFNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDTKIELLKFVQSEAQ
          SFQEVREYMFNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHD.KIEL.KFVQSEAQ
Retrocopy SFQEVREYMFNLFKALKRIHQFGIVHRDVKPSNFLYNRRLKKYALVDFGLAQGTHDIKIELFKFVQSEAQ

Parental  QERCSQNKSHIITGNKIPLSGPVPKELDQQSTTKASVKRPYTNAQIQIKQGKDGKEGSVGLSVQRSVFGE
          QERCSQNKSHIITGN.IPLSGPVPK.LDQQSTTKASVKRP.T.AQIQIKQGKDGKEGSVGLSVQRSVFG.
Retrocopy QERCSQNKSHIITGNRIPLSGPVPKDLDQQSTTKASVKRPCTKAQIQIKQGKDGKEGSVGLSVQRSVFGK

Parental  RNFNIHSSISHESPAVKLMKQSKTVDVLSRKLATKKKTISAKVMNSGVMRKTASSCPTSLTCDCYATDKV
          RNFNIHSSISHESPAVKLMKQSKTVDVLSRKLATKKK.ISAKVMNSGVMRK.ASSCP.SLTCDCYATDKV
Retrocopy RNFNIHSSISHESPAVKLMKQSKTVDVLSRKLATKKKVISAKVMNSGVMRKAASSCPASLTCDCYATDKV

Parental  CSICLSRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMT
          CSIC.SRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMT
Retrocopy CSICPSRRQQVAPRAGTPGFRAPEVLTKCPNQTTAIDMWSAGVIFLSLLSGRYPFYKASDDLTALAQIMT

Parental  IRGSRETIQAAKTFGKSILCSKEVPAQDLRKLCERLRGMDSNTPKLTSDIQGPASHQPTVSEKTDHKASR
          I.GSRET.QAAKTFGKSILCSKEVPAQDLRKLCERLRGMDSNTPK.TSDIQGP.SHQPT.SEKTDHKASR
Retrocopy IQGSRETMQAAKTFGKSILCSKEVPAQDLRKLCERLRGMDSNTPK*TSDIQGPTSHQPTISEKTDHKASR

Parental  LIQTPPGQYSGNSFKKGDSNSCGCCFDEYTTNLEGWNEVPDEAYDLLDKLLDLNPASRITAEEALLHPFF
          L.QTPPGQYSGNSFKKGDSNSCGCCFDEYTTNLEGWNEVPDEAYDLLDKLLDLNPASRITAEE.LLHPFF
Retrocopy LVQTPPGQYSGNSFKKGDSNSCGCCFDEYTTNLEGWNEVPDEAYDLLDKLLDLNPASRITAEEVLLHPFF

Parental  KDMSL
          KDMSL
Retrocopy KDMSL

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	9.52 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	3.65 RPM
SRP007412_cerebellum	0.00 RPM	10.40 RPM
SRP007412_heart	0.00 RPM	1.88 RPM
SRP007412_kidney	0.00 RPM	3.76 RPM
SRP007412_liver	0.00 RPM	1.19 RPM
SRP007412_testis	0.04 RPM	34.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1689 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006454	1 retrocopy	retro_dnov_2242,
Macaca mulatta	ENSMMUG00000011010	1 retrocopy	retro_mmul_1689 ,