RetrogeneDB ID: retro_mmul_1735

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:165409814..165410432(-)
• Located in intron of: ENSMMUG00000015432

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD2BP2
• Ensembl ID: ENSMMUG00000021844
• Aliases: None
• Description: CD2 antigen cytoplasmic tail-binding protein 2 [Source:RefSeq peptide;Acc:NP_001247625]

Sequence

>retro_mmul_1735
CAGGCCTCAGACTTGGAAGAGGAAGACAGCTTGGGCCAGACCCCAGTGACTGCCCAAGCCCTCTTGGAGGGACTTTTGGA
GCTCCTACTGTCTAGAGAGACAGTGGTTGGGGCACTGAGGCATCTGGGGGCCCAAGAAGAGGCAAAGGGAGCAGCAAGGG
GCCCAGGTGACCAAGTTCCCCGCAGCACCTGGATCGGCTCTCCGAGTTGGCTGACCAGATGGTGGCCCGGGGCAACCTTG
GCAGGCACCAGGAAATGAGGGAACAGTTGGCCATGCGGCTGAAGGGTTTGGAGTGCCAGGCCCTAGGGACCCCACAATCC
CACATCCCCACGCTCCCTGGACATGTTCACTGAGGAAGTGGTGGAGAGGGAACTGGAGACCCCAACCCCTACCCAGAAAG
AAGAAGCAGAGTTGCCACGAGATGGTCTGGTGGATGTGATGTGGGAATATAAGTGGGTGAACCTGGGGGATGCCAAGCTG
CATGGGCCCTTCACCAGCGCCCAGATGCAGACCTGGATGAGTGAAGGCTACTTTCCTGATGGTGTTTATTGCTGGAAGCT
GGACCCCCTTGGTGGTCAGTTCTACAACTCTAAATGCATTGACTTTGACCTCTACACC

Alignment

ORF - retro_mmul_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 60.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QASDSEEEDSLGQTPMSAQALLEGLLELLLPRETVAGALRRLGARGG-GKGSSKGPGRPSSPQRLDRLSG
          QASD.EEEDSLGQTP..AQALLEGLLELLL.RETV.GALR.LGA....GKGSSKGP..PSSPQ.LDRLS.
Retrocopy QASDLEEEDSLGQTPVTAQALLEGLLELLLSRETVVGALRHLGAQEE<GKGSSKGPR*PSSPQHLDRLSE

Parental  LADQMVARGNLGVYQETRERLAMRLKGLGCQTVG-PHNPTPPPSLDMFAEEVAEEELETPTPTQRGEAES
          LADQMVARGNLG..QE.RE.LAMRLKGL.CQ..G.PHNPT.P.SLDMF.EEV.E.ELETPTPTQ..EAE.
Retrocopy LADQMVARGNLGRHQEMREQLAMRLKGLECQALG>PHNPTSPRSLDMFTEEVVERELETPTPTQKEEAEL

Parental  PGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFELYT
          P.DGLVDVMWEYKW.N.GDA.L.GPFTSAQMQTW.SEGYFPDGVYC.KLDP.GGQFYNSK.IDF.LYT
Retrocopy PRDGLVDVMWEYKWVNLGDAKLHGPFTSAQMQTWMSEGYFPDGVYCWKLDPLGGQFYNSKCIDFDLYT

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	18.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	35.46 RPM
SRP007412_cerebellum	0.00 RPM	18.08 RPM
SRP007412_heart	0.00 RPM	24.91 RPM
SRP007412_kidney	0.00 RPM	28.52 RPM
SRP007412_liver	0.04 RPM	18.13 RPM
SRP007412_testis	0.08 RPM	16.17 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1735 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1735 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3900
Pan troglodytes	retro_ptro_2653
Gorilla gorilla	retro_ggor_2627
Pongo abelii	retro_pabe_3179

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169217	1 retrocopy	retro_hsap_3900,
Gorilla gorilla	ENSGGOG00000014271	1 retrocopy	retro_ggor_2627,
Macaca mulatta	ENSMMUG00000021844	1 retrocopy	retro_mmul_1735 ,
Nomascus leucogenys	ENSNLEG00000015767	1 retrocopy	retro_nleu_1139,
Pongo abelii	ENSPPYG00000007267	1 retrocopy	retro_pabe_3179,
Pan troglodytes	ENSPTRG00000007995	1 retrocopy	retro_ptro_2653,