RetrogeneDB ID: retro_mmul_1969

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:111037444..111038150(-)
• Located in intron of: ENSMMUG00000015259

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSMMUG00000007405
• Aliases: None
• Description: peptidyl-prolyl cis-trans isomerase FKBP4 [Source:RefSeq peptide;Acc:NP_001248268]

Sequence

>retro_mmul_1969
ATGACAGCTGAGGAGATGAAGGAGACCTAGAGCTGGGAGCAATTGGTGCCTCTGCCCATGGAGGGAGTGGACATTAGCCC
CAAACAGGAGGAAGGCATGCTGAAAGTCATCGAGAGAGGGCACAGGTACAGAGATGCCCATGATTGGGGACCGAGTCTTT
GTCCACTACACTGGCTGGCTGTTAGATGGCACAAACTTTGACCCCAGTCTGGATCACTCCTTTGACTTGGGAAAAGGGAG
ATCATCAAGGCTTGGGATATTGCTATAGCAGCCATGAAGGTGGGGGAGGTGTGCCATATCACCTGCAAACCAGAATATGC
CTACAGTGCAGTAGGCAGTCCTCCAAAGGTCTCCCCATTGCGACGCTTGTGTTTGAGGTGGAGTTGTTTCAGTTTAAGGG
AGAAGATCTGATGGAAGAGGAATATGGTGGAATCACCTAGAGAACACAGACTCGTGGTGAAGGCTATCCAGGCCCAGTGA
GGGTGCTATCATGGAGGTTGCACTGGAAGGGTGCTACAAGGACCAGCCCTTTGAACATCAGGAGCTCTGCTTTGAGGCAG
GCAAGGGGGAGAACTTGGATTTGCCTTATGGTCTGAGGAGGGCCATTCAGTGCATGTAGAAAGGAGAACATCCCATTGTG
TACCTCAAACCCAGCTATGCTTTTGGCAGTGTTGGGACGGAAAAGTTCCAAATCCCACAAAATGCC

Alignment

ORF - retro_mmul_1969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.47 %
• Parental protein coverage: 52.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTAEEMKAAESGAQSAPLPIEGVD-ISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDS
          MTAEEMK...S..Q..PLP.EGVD...P.......K...REGTGTEMPMIGDRVFVHYTGWLLDGT.FD.
Retrocopy MTAEEMKET*SWEQLVPLPMEGVD>LAPNRRKAC*KS-SREGTGTEMPMIGDRVFVHYTGWLLDGTNFDP

Parental  SLDRKDKFSFDLGKG-EVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKIPPS-ATLVFEVSLFEF
          SLD.....SFDLGKG.E.IKAWDIAIA.MKVGEVCHITCKPEYAY...GSPPK..P..ATLVFEV.LF.F
Retrocopy SLDH----SFDLGKG<EIIKAWDIAIAAMKVGEVCHITCKPEYAYSAVGSPPKVSPL<ATLVFEVELFQF

Parental  KGEDLTEEEDGGIIRRIRTRGEGY-AKPNEGAIVEVALEGYYKDQLFDQRELRFEIGEGENLDLPYGLER
          KGEDL.EEE.GGI..R..TRGEGY...P.EGAI.EVALEG.YKDQ.F...EL.FE.G.GENLDLPYGL.R
Retrocopy KGEDLMEEEYGGIT*RTQTRGEGY<SRPSEGAIMEVALEGCYKDQPFEHQELCFEAGKGENLDLPYGLRR

Parental  AIQRMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNA
          AIQ.M.KGEH.IVYLKPSYAFGSVG.EKFQIP.NA
Retrocopy AIQCM*KGEHPIVYLKPSYAFGSVGTEKFQIPQNA

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	92.55 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	144.22 RPM
SRP007412_cerebellum	0.19 RPM	212.45 RPM
SRP007412_heart	0.00 RPM	59.00 RPM
SRP007412_kidney	0.00 RPM	67.96 RPM
SRP007412_liver	0.00 RPM	109.29 RPM
SRP007412_testis	0.04 RPM	281.61 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1969 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
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	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,