RetrogeneDB ID: retro_mmul_225

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:92628366..92630112(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000000126
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000008835
• Aliases: None
• Description: None

Sequence

>retro_mmul_225
ATGGCGGTGCGACAGGCGCTAGGCCGCGGCCTGCAGCTGGGTCGAGAGCTGCTGCTGCGCTTCACCGGCAAGCCGGGCCG
GGCCTACGGCTTGGGGCGGCCGGGCCCGGCGGCGGGCTGTGTGCGCGGGGAGCGTCCGGGCTGGGCCGCAGGACCGGGAG
CGGAGCCTCGCAGGATCGGTCTCGGGCTCCCCAACCGCCTCCGCTTCTTTCGCCAGTCGGTGGCCGGGCTGGCGGCGCGG
TTGCAGCGGCAGTTCCTGGTGCGGGCCTGGGGCTGCGCGGGCCCTTGCGGCCGGGCAGTCTTTCTGGCCTTCGGGCTAGG
GCTGGGCCTCATCGAGGAGAAGCAGGCGGAGAGCCGACGGGCGGTCTCGGCCTGTCAGGAGATCCAGGCAATTTTTACCC
AGAAAAGCAAGCCAGGGCCTGACCCGTTGGACACAAGACGCTGGCAGGGCTTTCGGCTGGAGGAGTATCTGATAGGGCAG
TCCATTGGCAAGGGCTGCAGTGCCGCTGTGTATGAAGCCACCATGCCTGCATTGCCCCAGAACCTGGAGGTGACAAAGAG
CACCGGGTCGCTTCCAGGGAGAGGCCCAGGTACCAGTGCACCAGGAGAAGAGCAGGAGCAAGCTCTGGGGGCCCCTGCCT
TCCCCTTGGCCATCAAGATGATGTGGAACATCTCGGCAGGTTCCTCCAGCGAAGCTATCTTGAACACAATGAGCCAGGAG
CTGGTCCCAGCGAGCCGAGTGGCCTTGGCCGGGGAGTATGGAGCAGTCACTTACAGAAAATCCAAGAGAGGTCCCAAGCA
ACTAGCCCCTCACCCCAACATCATCCGGGTTCTCCGCGCTTTCACCTCTTCCGTGCCGCTGCTACCCGGGGCCCTGGTTG
ACTACCCTGATGTGCTGCCCCCACGCCTCCACCCTGAAGGCCTGGGCCACGGCCGGACGCTGTTCCTCGTTATGAAGAAC
TATCCCTGTACCCTGCGCCAGTACCTTCGCGCGAACACACCCAGCCCCCGCCTCGCCACCATGATGATGCTGCAGCTGCT
GGAAGGCGTGGACCATCTGGTTCAACAGGGCATCGCGCACAGAGACCTGAAATCCGACAACATCCTTGTGGAGCTGGACC
CAGACGGCTGCCCCTGGCTGGTGATCGCAGATTTTGGCTGCTGCCTGGCTGATGAGAGCATCGGCCTGCAGTTGCCCTTC
AGCAGCTGGTATGTGGATCGGGGCGGAAACGGCTGCCTGATGGCCCCAGAGGTGTCCACGGCCCGTCCTGGCCCCAGGGC
AGTGATTGACTACAGCAAGGCTGATGCCTGGGCAGTGGGAGCCATCGCCTATGAAATCTTCGGGCTTGTCAATCCCTTCT
ACAGCCAGGGCAAGGCCCACCTTGAGAGCCGCAGCTACCAGGAGGCTCAGCTACCTGCACTGCCCGAGTCGGTGCCTCCA
GACGTGAGACAGCTGGTGAGGGCACTGCTCCAGCGAGAGGCCAGCAAGAGACCATCTGCCCGAGTAGCTGCAAATGTGCT
TCATCTAAGCCTCTGGGGTGAACAGATTCTAGCCCTGAAGAATCTGAAGTTAGATAAGATGGTTGGCTGGCTTCTCCAAC
AATCGGCTGCCACTTTGTTGGCCAACAGGCTCACAGAGAAGTGTTGTGTGGAAACAAAAATGAAGATGCTCTTTCTGGCT
AACCTGGAGTGTGAAACGCTCTGCCAGGCAGCCCTCCTTCTCTGCTCATGGAGGGCAGCCCTGTGA

Alignment

ORF - retro_mmul_225 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVRQALGRGLQLGRELLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRIGLGLPNRLRFF
          MAVRQALGRGLQLGRELLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRIGLGLPNRLRFF
Retrocopy MAVRQALGRGLQLGRELLLRFTGKPGRAYGLGRPGPAAGCVRGERPGWAAGPGAEPRRIGLGLPNRLRFF

Parental  RQSVAGLAARLQRQFLVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRRAVSACQEIQAIFTQKSKPGP
          RQSVAGLAARLQRQFLVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRRAVSACQEIQAIFTQKSKPGP
Retrocopy RQSVAGLAARLQRQFLVRAWGCAGPCGRAVFLAFGLGLGLIEEKQAESRRAVSACQEIQAIFTQKSKPGP

Parental  DPLDTRRWQGFRLEEYLIGQSIGKGCSAAVYEATMPALPQNLEVTKSTGSLPGRGPGTSAPGEEQEQALG
          DPLDTRRWQGFRLEEYLIGQSIGKGCSAAVYEATMPALPQNLEVTKSTGSLPGRGPGTSAPGEEQEQALG
Retrocopy DPLDTRRWQGFRLEEYLIGQSIGKGCSAAVYEATMPALPQNLEVTKSTGSLPGRGPGTSAPGEEQEQALG

Parental  APAFPLAIKMMWNISAGSSSEAILNTMSQELVPASRVALAGEYGAVTYRKSKRGPKQLAPHPNIIRVLRA
          APAFPLAIKMMWNISAGSSSEAILNTMSQELVPASRVALAGEYGAVTYRKSKRGPKQLAPHPNIIRVLRA
Retrocopy APAFPLAIKMMWNISAGSSSEAILNTMSQELVPASRVALAGEYGAVTYRKSKRGPKQLAPHPNIIRVLRA

Parental  FTSSVPLLPGALVDYPDVLPPRLHPEGLGHGRTLFLVMKNYPCTLRQYLRANTPSPRLATMMMLQLLEGV
          FTSSVPLLPGALVDYPDVLPPRLHPEGLGHGRTLFLVMKNYPCTLRQYLRANTPSPRLATMMMLQLLEGV
Retrocopy FTSSVPLLPGALVDYPDVLPPRLHPEGLGHGRTLFLVMKNYPCTLRQYLRANTPSPRLATMMMLQLLEGV

Parental  DHLVQQGIAHRDLKSDNILVELDPDGCPWLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVST
          DHLVQQGIAHRDLKSDNILVELDPDGCPWLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVST
Retrocopy DHLVQQGIAHRDLKSDNILVELDPDGCPWLVIADFGCCLADESIGLQLPFSSWYVDRGGNGCLMAPEVST

Parental  ARPGPRAVIDYSKADAWAVGAIAYEIFGLVNPFYSQGKAHLESRSYQEAQLPALPESVPPDVRQLVRALL
          ARPGPRAVIDYSKADAWAVGAIAYEIFGLVNPFYSQGKAHLESRSYQEAQLPALPESVPPDVRQLVRALL
Retrocopy ARPGPRAVIDYSKADAWAVGAIAYEIFGLVNPFYSQGKAHLESRSYQEAQLPALPESVPPDVRQLVRALL

Parental  QREASKRPSARVAANVLHLSLWGEQILALKNLKLDKMVGWLLQQSAATLLANRLTEKCCVETKMKMLFLA
          QREASKRPSARVAANVLHLSLWGEQILALKNLKLDKMVGWLLQQSAATLLANRLTEKCCVETKMKMLFLA
Retrocopy QREASKRPSARVAANVLHLSLWGEQILALKNLKLDKMVGWLLQQSAATLLANRLTEKCCVETKMKMLFLA

Parental  NLECETLCQAALLLCSWRA
          NLECETLCQAALLLCSWRA
Retrocopy NLECETLCQAALLLCSWRA

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	6.39 RPM	1.01 RPM
SRP007412_brain_prefrontal_cortex	1.67 RPM	57.75 RPM
SRP007412_cerebellum	1.03 RPM	0.45 RPM
SRP007412_heart	6.07 RPM	3.89 RPM
SRP007412_kidney	4.93 RPM	0.94 RPM
SRP007412_liver	7.05 RPM	10.45 RPM
SRP007412_testis	0.72 RPM	12.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_225 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_225 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_225 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006493	1 retrocopy	retro_cjac_1024,
Macaca mulatta	ENSMMUG00000008835	1 retrocopy	retro_mmul_225 ,
Nomascus leucogenys	ENSNLEG00000007921	1 retrocopy	retro_nleu_3022,