RetrogeneDB ID: retro_mmul_2349

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:72422101..72422988(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BAG4
• Ensembl ID: ENSMMUG00000013775
• Aliases: None
• Description: None

Sequence

>retro_mmul_2349
GCACCTGATTATACTCAGACCTGTTACTCCACAGAAGTTACAAATACTTACCGTTCACCTGGCAACAGCCCAACTCCAGT
CTCTCGTTGAGTCTATTCTCGGCAGGACTGTCAGACTGAAGTACCCTCTCTTAGGCGGCAGGTTGCAGGGTATCCGGCTT
CACAGAACCCTGGAATGACCCTGCCCCATTATCGTTATGGAGATGGTAATCGTAGTGTTCCACAATCAGGACAAATTGTA
CTACCACAAGAAGATGCGTGGCCTTCTCCTGGTGCTTATGGAATGGGTGGCCATTATCCTTGGCCTTCATCAGCGCCCTC
AGCACCGCCTGGCAATCTCTACATGACCGGAGGTACTTCACCATGGCCTAGCAGTGGCTCTCCTCAGTCACCACCTACAC
CCCCACTCCAGCAGCCCAAGGATTCTTCACACCCCTGCAGCCAATCAGATCAAAGCATGAACCGGTACAACTTCCCTTGC
AGTGTCCATCAGTATGAATCCTTGGGGACAGTGAACAAGAATGATTCAGATCTTTTGGATTCCCAAGTCCAGTATAGCGC
TGAGCCTCAGCTGTATGGTAATGCCACCAGTGACCATCCCAACAGTCAAGATTAAAGTAGCAGTCTTCCTGAAGAATGTG
TACCTTCAGATGAAAGTACTCCTCCGAGTATTACAAAACCATTCATGTGCTGGAGAAGGTCCAGTATCTTGAACAAGAAG
TAGAAGAATTTGTAGGAAAAAAGATAGACTAAACATACTGGCTTCTGGAAGAAACGCTAACCAAGAAACTTTTGGAACTG
GATTCAGTTGAAACTGGGGACGAGGACTCTGTATGGCAGGCCAGAAAAGAGGCTGTTTGTAAGATTCAGGCCATACTGGA
AAAATTA

Alignment

ORF - retro_mmul_2349 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 64.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APGYTQTSYSTEVPSTYRSSGNSPTPVSRWIYPQQDCQTEAPPLRGQVPGYPASQNPGMTLPHYPYGDGN
          AP.YTQT.YSTEV..TYRS.GNSPTPVSR..Y..QDCQTE.P.LR.QV.GYPASQNPGMTLPHY.YGDGN
Retrocopy APDYTQTCYSTEVTNTYRSPGNSPTPVSR*VYSRQDCQTEVPSLRRQVAGYPASQNPGMTLPHYRYGDGN

Parental  RSVPQSGPTVRPQEDAWASPGAYGMGGRYPWPSSAPSAPPGNLYMTESTSPWPSSGSPQSPPSPPLQQPK
          RSVPQSG..V.PQEDAW.SPGAYGMGG.YPWPSSAPSAPPGNLYMT..TSPWPSSGSPQSPP.PPLQQPK
Retrocopy RSVPQSGQIVLPQEDAWPSPGAYGMGGHYPWPSSAPSAPPGNLYMTGGTSPWPSSGSPQSPPTPPLQQPK

Parental  DSSYPYSQSEQSMNRHNFPCSVHQYESSGTVNNDDSDLLDCQVQYSAEPQLYGDATSDHPNNQDQSSSLP
          DSS.P.SQS.QSMNR.NFPCSVHQYES.GTVN..DSDLLD.QVQYSAEPQLYG.ATSDHPN.QD.SSSLP
Retrocopy DSSHPCSQSDQSMNRYNFPCSVHQYESLGTVNKNDSDLLDSQVQYSAEPQLYGNATSDHPNSQD*SSSLP

Parental  EERVPSDESTPPSIK-KIIHVLEKVQYLEQEVEEFVGKKTDKAYWLLEEMLTKELLELDSVETGGQDSVR
          EE.VPSDESTPPSI..K.IHVLEKVQYLEQEVEEFVGKK.D..YWLLEE.LTK.LLELDSVETG..DSV.
Retrocopy EECVPSDESTPPSIT<KTIHVLEKVQYLEQEVEEFVGKKID*TYWLLEETLTKKLLELDSVETGDEDSVW

Parental  QARKEAVCKIQAILEKL
          QARKEAVCKIQAILEKL
Retrocopy QARKEAVCKIQAILEKL

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	34.51 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	35.62 RPM
SRP007412_cerebellum	0.00 RPM	39.65 RPM
SRP007412_heart	0.00 RPM	5.77 RPM
SRP007412_kidney	0.00 RPM	12.21 RPM
SRP007412_liver	0.00 RPM	5.74 RPM
SRP007412_testis	0.49 RPM	6.45 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2349 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2349 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2349 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
Bos taurus	ENSBTAG00000013143	1 retrocopy	retro_btau_1772,
Homo sapiens	ENSG00000156735	1 retrocopy	retro_hsap_4072,
Macaca mulatta	ENSMMUG00000013775	1 retrocopy	retro_mmul_2349 ,