RetrogeneDB ID: retro_mmul_1609

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:60878620..60878869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSTB
• Ensembl ID: ENSMMUG00000012303
• Aliases: CSTB, cystatin-B
• Description: cystatin-B [Source:RefSeq peptide;Acc:NP_001244627]

Sequence

>retro_mmul_1609
TGCTGGGCGCCCTTAGGCACGCAGCTGGCCAGCCGGGAGACCCAGGACATCGTGGACCAGGTGAGGGCCCAGCTTGAAGA
GAAAGAAAAGAAGTTCCCTGTGTTTAAGGCTGTGTCGTTCAAGAGGGTTGTGAGGACAAACTGCTTCATCAAGATGTACA
TTGGTGACGAGGACTTCATACATTTGGGAGTATTCAGAAGTCTCCCTCACAAAAACAAACCCTTGATCTTGTCTAACTAC
CAGACCAAC

Alignment

ORF - retro_mmul_1609 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 87.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CGAPSAVQPATAETQDIADQVRSQLEEKENKKFPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHLRVFKS
          C.AP...Q.A..ETQDI.DQVR.QLEEKE.KKFPVFKAVSFK...V..TN.FIK...GDEDF.HL.VF.S
Retrocopy CWAPLGTQLASRETQDIVDQVRAQLEEKE-KKFPVFKAVSFKR--VVRTNCFIKMYIGDEDFIHLGVFRS

Parental  LPHENKPLTLSDYQTN
          LPH.NKPL.LS.YQTN
Retrocopy LPHKNKPLILSNYQTN

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	42.80 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	54.10 RPM
SRP007412_cerebellum	0.00 RPM	25.57 RPM
SRP007412_heart	0.00 RPM	32.39 RPM
SRP007412_kidney	0.00 RPM	62.32 RPM
SRP007412_liver	0.00 RPM	33.37 RPM
SRP007412_testis	0.00 RPM	13.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1609 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1609 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1609 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000524	1 retrocopy	retro_btau_97,
Loxodonta africana	ENSLAFG00000002664	1 retrocopy	retro_lafr_370,
Myotis lucifugus	ENSMLUG00000022457	1 retrocopy	retro_mluc_379,
Macaca mulatta	ENSMMUG00000012303	1 retrocopy	retro_mmul_1609 ,
Otolemur garnettii	ENSOGAG00000006101	2 retrocopies	retro_ogar_3274, retro_ogar_3275,
Pteropus vampyrus	ENSPVAG00000007022	1 retrocopy	retro_pvam_1089,
Rattus norvegicus	ENSRNOG00000001201	1 retrocopy	retro_rnor_551,
Sarcophilus harrisii	ENSSHAG00000017952	3 retrocopies	retro_shar_229, retro_shar_623, retro_shar_699,