RetrogeneDB ID: retro_mmul_2171

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:104764733..104764996(+)
• Located in intron of: ENSMMUG00000011997

Retrocopy information

• Ensembl ID: ENSMMUG00000001281
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSMMUG00000012341
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase FKBP1B [Source:RefSeq peptide;Acc:NP_001253652]

Sequence

>retro_mmul_2171
AAGAAGAGCCAGATGTGTGTGGTGCACTACACAGGAATGTTCCAAAATGGGAATAAATTTGATTTATCCCAAGACAGAAA
CAAGTTCAAAACTGGTGAACAGGAAGTCATCAATGGTTTTGAAGAGGACATAGTGCAGATGAGCCTGGGGCAGAAGGTGA
AGCTGACTTGCATACCTGATGTGTCATATGGAGCCCCAGGCTTCTCTTGTGTCATCCCTCCCAGTGCTACCCTGTCTTTG
ACAGGGAGCTGCTCAACTCAGAG

Alignment

ORF - retro_mmul_2171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.48 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATG
          KK.Q.CVVHYTGM.QNG.KFD.S.DRN...KF..G.QEVI.GFEE...QMSLGQ..KLTC.PDV.YGA.G
Retrocopy KKSQMCVVHYTGMFQNGNKFDLSQDRN---KFKTGEQEVINGFEEDIVQMSLGQKVKLTCIPDVSYGAPG

Parental  HPGVIPPNATL-IFDVELLNLE
          ...VIPP.ATL..FD.ELLN.E
Retrocopy FSCVIPPSATL<VFDRELLNSE

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	7.28 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	16.50 RPM
SRP007412_cerebellum	0.13 RPM	4.65 RPM
SRP007412_heart	0.00 RPM	0.06 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.04 RPM
SRP007412_testis	0.04 RPM	0.15 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2171 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2171 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2171 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1329
Pan troglodytes	retro_ptro_906
Gorilla gorilla	retro_ggor_1036
Pongo abelii	retro_pabe_1105
Callithrix jacchus	retro_cjac_696

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Macaca mulatta	ENSMMUG00000009587	1 retrocopy	retro_mmul_552,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171 ,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Macaca mulatta	ENSMMUG00000016512	2 retrocopies	retro_mmul_2094, retro_mmul_735,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,