RetrogeneDB ID: retro_mmul_1179

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:41503317..41504082(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC2
• Ensembl ID: ENSMMUG00000004412
• Aliases: None
• Description: None

Sequence

>retro_mmul_1179
AAAGAGGCAAGAAGACATGAATCCAAAGAAAAATCCTCTAAGAAACACAAATCTGAGGAACATAATGACAAAGAACATTC
CTCTGATAAAGAAAGAGAGCAACTAAATTAATCTGAAAATAGTGAGGACAAGCACAAATGCAAAAAATGAAAGTCATCAA
GAGGCAGAAGTCACTCAAGATCTAGGTCTCGTGAAAGACGCCATTGTAGTAGAAGCAGGCTGGAGCAGAAGTCTCGATCC
AGGAGTGGGGAGTGGAAGAAGTCTCAACCTAGAAGCAGAGAGGGGAAGAAATCAAGATCCAGAAGCAGGGAAAGAAAAGG
GCATATCAGATCTCATTCCTGCTCAAGATCGAGACACAGGCATAGGACTAGAAGCAGGAGTAGAACAAAGAGTAGGAGTC
GAGATAGAAAAAAGAGAATTGAAAAACCGAGAAGATTTAGCAGAAGTTAAAGCTGGACTCCGAGTCCACTTCCCTTCAGA
AGCAGAAACACAGCAATAGACACACAAGAAGCTTTAGCTAGGAGGTTGGAAAGGGCAAAGAAATTATAAGAACAGCGATA
CAAGAAAATGGTTGAAAAACAAAAACAACAAGAAATAACTGCAGCAGCTGCAGCTACTGGGGGTTCTGTTCTCAATGTTG
CTGCCCTGTTGGCATCAGGAATGCAAGTAATACCTCAGATAGCCATGACAGCTCAAATGGCAGCCCTGCAAGCTAAAGCT
TTGGCAGAGACAGGAATAGCTGTACCTAGCTACTATAACCCAGCA

Alignment

ORF - retro_mmul_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.71 %
• Parental protein coverage: 77.68 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQARRHESKDKSSKKHKSEEHNDKEHSSDKGRERLNSSENGEDRHKRKERKSSRGRSHSRSRSRERVHFY
          K.ARRHESK.KSSKKHKSEEHNDKEHSSDK.RE.LN.SEN.ED.HK.K..KSSRGRSHSRSRSRER.H..
Retrocopy KEARRHESKEKSSKKHKSEEHNDKEHSSDKEREQLN*SENSEDKHKCKK*KSSRGRSHSRSRSRERRHCS

Parental  RSRERKKSRSRSRERKKSRSRSRERKKSRSRSRERKRRIRSRSRSRSRHRHRTRSRSRTRSRSRDRKKRI
          RSR...KSRSRS.E.KKS..RSRE.KKSRSRSRERK..IRS.S.SRSRHRHRTRSRSRT.SRSRDRKKRI
Retrocopy RSRLEQKSRSRSGEWKKSQPRSREGKKSRSRSRERKGHIRSHSCSRSRHRHRTRSRSRTKSRSRDRKKRI

Parental  EKPRRFSRSLSRTPSPPPFRGRNTAMDAQEALARRLERAKKLQEQREKEMVEKQKQQEI-AAAAATGGSV
          EKPRRFSRS.S.TPSP.PFR.RNTA.D.QEALARRLERAKKL.EQR.K.MVEKQKQQEI.AAAAATGGSV
Retrocopy EKPRRFSRS*SWTPSPLPFRSRNTAIDTQEALARRLERAKKL*EQRYKKMVEKQKQQEITAAAAATGGSV

Parental  LNVAALLASGTQVTPQIAMAAQMAALQAKALAETGIAVPSYYNPA
          LNVAALLASG.QV.PQIAM.AQMAALQAKALAETGIAVPSYYNPA
Retrocopy LNVAALLASGMQVIPQIAMTAQMAALQAKALAETGIAVPSYYNPA

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	2.69 RPM	47.96 RPM
SRP007412_brain_prefrontal_cortex	0.40 RPM	28.24 RPM
SRP007412_cerebellum	2.00 RPM	48.11 RPM
SRP007412_heart	1.41 RPM	32.03 RPM
SRP007412_kidney	2.70 RPM	32.04 RPM
SRP007412_liver	0.40 RPM	9.62 RPM
SRP007412_testis	3.43 RPM	59.07 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1179 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1179 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
Callithrix jacchus	ENSCJAG00000020419	1 retrocopy	retro_cjac_468,
Dasypus novemcinctus	ENSDNOG00000008912	1 retrocopy	retro_dnov_303,
Macaca mulatta	ENSMMUG00000004412	1 retrocopy	retro_mmul_1179 ,
Mus musculus	ENSMUSG00000029422	1 retrocopy	retro_mmus_2465,
Rattus norvegicus	ENSRNOG00000001238	1 retrocopy	retro_rnor_1536,