RetrogeneDB ID: retro_mmul_2397

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 9:45352990..45353343(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANKRD54
• Ensembl ID: ENSMMUG00000015254
• Aliases: None
• Description: None

Sequence

>retro_mmul_2397
ATTGTGGCCTGCACCGACCATGACTCTGTCATCACCTTACTGCTACGACGAGGGACCCGGTGGATGTCCTGGACCAAGCT
GGACGTATGCCTCCACACCTGGCCAAGACGAAGCAGAACATCCTGCAGGACGACCACTCCCAGTGCCTGGAGGCTGTGCG
ACTGGAGGTGAAGCAGATCATCCCAATGCTGAGGAAGAACCCAGTGCACCTACAGTGACGTGAACAGCGGAAATGGTTGG
ACCACCTCTGCACCCACCTCTAGATGACCAGTACCAAAGAGCAGGTGGATGAAGTGCCCGACCTCCCAGCCAGCTCCACC
TCGCTCAGTCTTTGGATACAGAGCATGGAGGAG

Alignment

ORF - retro_mmul_2397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.07 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAACTNHVPVITTLLRGGAR-VDALDRAGRTPLHLAKSKLNILQEGHAQCLEAVRLEVKQIIHMLREYLE
          ..ACT.H..VIT.LLR.G.R.VD.LD.AGR.P.HLAK.K.NILQ..H.QCLEAVRLEVKQII.MLR....
Retrocopy IVACTDHDSVITLLLRRGTR<VDVLDQAGRMPPHLAKTKQNILQDDHSQCLEAVRLEVKQIIPMLRKNPV

Parental  RLGQHEQRERLDDLCTRLQMTSTKEQVDEVTDLLASFTSLSLQMQSMEK
          .L...EQR..LD.LCT.L.MTSTKEQVDEV.DL.AS.TSLSL..QSME.
Retrocopy HLQ*REQRKWLDHLCTHL*MTSTKEQVDEVPDLPASSTSLSLWIQSMEE

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	3.14 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.15 RPM
SRP007412_cerebellum	0.00 RPM	6.97 RPM
SRP007412_heart	0.00 RPM	3.12 RPM
SRP007412_kidney	0.00 RPM	7.75 RPM
SRP007412_liver	0.00 RPM	9.14 RPM
SRP007412_testis	0.75 RPM	18.70 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2397 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2397 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013953	1 retrocopy	retro_meug_1876,
Macaca mulatta	ENSMMUG00000015254	2 retrocopies	retro_mmul_2397 , retro_mmul_2444,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Sarcophilus harrisii	ENSSHAG00000009125	1 retrocopy	retro_shar_66,