RetrogeneDB - Retrocopy retro_mmul

                        
>retro_mmul_2377
TCAGGGCTCACCTGACTGCCCCTGAAGCAGCCAGAGCCCACCAGAGCCCCTCAGGGGACAGCGATCCCCTGAGGTATCCC

GGGGCCACCACCGGGCCACGGAGCAGCACTCCAGCCCCACTCCAGGGTCATTTTTTGCCCTCTCCCATCTGAGCAGTGTT

ACCAGGCCCCAGGGGGACCTGAGAATTAGGGCCGGCCTGGGTGGGGTCCCATGGAGTACTCCAGCGCACTCAGGGGCTCC

CTGCAGACGGGGGGCCTTCGCCCCGGAAGCCTGGACGCTGAGATAGACTTGCTGAGCAGCACGCTGGCCGAGCTGAAGGG

GGGTCGGGGTCATGCGCCCCTGCGACCAGACCAACAGGCAGAGCCCCGGCCACCTCCTGCCTCCCGCCCGGGCTCTCTGA

AGCCGAACCCAGCCTCGCGCTCCCAGCGTCTCCCTATGGGGCCCCACTGCAGCCTCTTATGCTGCCGCCAGCCCCCCCGG

CCGGCCTTCCCCGTGCAAGCAAAGGTGGCACAGTCAGTGAGGGGCTGCGGCCCACCCAGGCGGGGAACCTCTCAGGCCTC

TGGGCCCCTCCCGGGCCCCCACTTTCTGTCCCAGGCCAAGGTGAAGTCTGGGGGCCTGGCTATAGGAGCCAGAGAGAGCC

AGGGCCGGGGGCCAAAGAGGAAGCTGCGGGGGTCTCTGGCCCCGCAGGAGGAGGAAGAGGACGCGAGCACGGCCCCAGGT

GCCCCTGAGCCACCTCGGGAGGATGAGCTTGTCAGGCTGTCGAAGAAGCAGGTGCACGACATGAACCACCCGCCCAGCTG

GGAGTACTTTGGCCAGTGTGGTGGCTGCGGAGATGTGGTCGGGGATGGGGCTGGGGTTGTGGCCCTCGATTGCGTCTTTC

ATGTGGGCTGTTTTGTGTGTTCTACATGCCGGGCCCAGCTTCGGGGACAGCATTTCTACGCCATGGAGAGAGGGCGTGTT

GCCAGGGCTGCTACGTGGCCACCCGGGAGAAATGTGCCACGTGCTCCCAGCCCACCCTGGACCGGATCCTGCGGGCTATG

GGGAAGGACTACCACCCCAGCTGCTTCACC

ORF - retro_mmul_2377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.65 %
Parental protein coverage:	76.26 %
Number of stop codons detected:	2
Number of frameshifts detected:	10

Retrocopy - Parental Gene Alignment:

                                ParentalSGPTWLPPKQPEPARAPQGRAIPRGTPGPPPAHGAALQPHPRVNFCPLPSEQCYQAPGGPE-DRGPAWVG
SG.T.LP.KQPEP.RAPQG.AIP.G.PGPPP.HGAALQPH.RV.FCPLPSEQCYQAPGGPE...GPAWVG
RetrocopySGLT*LPLKQPEPTRAPQGTAIP*GIPGPPPGHGAALQPHSRVIFCPLPSEQCYQAPGGPE<ELGPAWVG
ParentalSHGVLQRTQGL-PADRG-GLRPGSLDAEIDLLSSTLAELNGGRGHVPRRPERQAYEPLPPPAYRTGSLKP
SHGVLQRTQGL.P..RG.GLRPGSLDAEIDLLSSTLAEL.GGRGH.P.RP..QA.EP.PPPA.R.GSLKP
RetrocopySHGVLQRTQGL<PCRRG<GLRPGSLDAEIDLLSSTLAELKGGRGHAPLRPDQQA-EPRPPPASRPGSLKP
ParentalNPAS-PLPASPYG-GPTPASYATASTPAG-PAFPVQVKVAQPVRGCGPPRRGASQASGPLPGPHF-PLPG
NPAS..LPASPYG.GPT.ASYA.AS.P.G.PAFPVQ.KVAQ.VRGCGPPRRG.SQASGPLPGPHF...PG
RetrocopyNPAS<ALPASPYG<GPTAASYAAAS-PPG<PAFPVQAKVAQSVRGCGPPRRGTSQASGPLPGPHF<SVPG
ParentalRGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGGEHG-PQVHLSQ-PPEDELDRLTKKLVHDMNHPPS
.GEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRG.EHG.PQV.LS..P.EDEL.RL.KK.VHDMNHPPS
RetrocopyQGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGREHG<PQVPLSH<PREDELVRLSKKQVHDMNHPPS
ParentalGEYFGQCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVER-RAYCEGCYVATLEKCAT
.EYFGQCGGCG.DVVGDGAGVVALD.VFHVGCFVCSTCRAQLRGQHFYA.ER.RA.C.GCYVAT.EKCAT
RetrocopyWEYFGQCGGCG-DVVGDGAGVVALDCVFHVGCFVCSTCRAQLRGQHFYAMER<RACCQGCYVATREKCAT
ParentalCSQPILDRILRAMGKAYHPGCFT
CSQP.LDRILRAMGK.YHP.CFT
RetrocopyCSQPTLDRILRAMGKDYHPSCFT

                            

                            Legend:
                            
                                *Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

                        

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0 .00 RPM	2 .69 RPM
SRP007412_brain_prefrontal_cortex	0 .16 RPM	7 .70 RPM
SRP007412_cerebellum	0 .00 RPM	4 .84 RPM
SRP007412_heart	0 .00 RPM	11 .07 RPM
SRP007412_kidney	0 .00 RPM	10 .45 RPM
SRP007412_liver	0 .00 RPM	2 .38 RPM
SRP007412_testis	0 .04 RPM	7 .16 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_2377 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2377 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_2377 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024772	1 retrocopy	retro_btau_1521,
Macaca mulatta	ENSMMUG00000021252	1 retrocopy	retro_mmul_2377 ,
Macaca mulatta	ENSMMUG00000032243	2 retrocopies	retro_mmul_1095, retro_mmul_2635,

	RetrogeneDB ID:	retro_mmul_2377
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	8:147564947..147566017(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMMUG00000016079
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	TRIP6
	Ensembl ID:	ENSMMUG00000021252
	Aliases:	None
	Description:	None

Parental	SGPTWLPPKQPEPARAPQGRAIPRGTPGPPPAHGAALQPHPRVNFCPLPSEQCYQAPGGPE-DRGPAWVG
	SG.T.LP.KQPEP.RAPQG.AIP.G.PGPPP.HGAALQPH.RV.FCPLPSEQCYQAPGGPE...GPAWVG
Retrocopy	SGLTLPLKQPEPTRAPQGTAIPGIPGPPPGHGAALQPHSRVIFCPLPSEQCYQAPGGPE<ELGPAWVG

Parental	SHGVLQRTQGL-PADRG-GLRPGSLDAEIDLLSSTLAELNGGRGHVPRRPERQAYEPLPPPAYRTGSLKP
	SHGVLQRTQGL.P..RG.GLRPGSLDAEIDLLSSTLAEL.GGRGH.P.RP..QA.EP.PPPA.R.GSLKP
Retrocopy	SHGVLQRTQGL<PCRRG<GLRPGSLDAEIDLLSSTLAELKGGRGHAPLRPDQQA-EPRPPPASRPGSLKP

Parental	NPAS-PLPASPYG-GPTPASYATASTPAG-PAFPVQVKVAQPVRGCGPPRRGASQASGPLPGPHF-PLPG
	NPAS..LPASPYG.GPT.ASYA.AS.P.G.PAFPVQ.KVAQ.VRGCGPPRRG.SQASGPLPGPHF...PG
Retrocopy	NPAS<ALPASPYG<GPTAASYAAAS-PPG<PAFPVQAKVAQSVRGCGPPRRGTSQASGPLPGPHF<SVPG

Parental	RGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGGEHG-PQVHLSQ-PPEDELDRLTKKLVHDMNHPPS
	.GEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRG.EHG.PQV.LS..P.EDEL.RL.KK.VHDMNHPPS
Retrocopy	QGEVWGPGYRSQREPGPGAKEEAAGVSGPAGGGRGREHG<PQVPLSH<PREDELVRLSKKQVHDMNHPPS

Parental	GEYFGQCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVER-RAYCEGCYVATLEKCAT
	.EYFGQCGGCG.DVVGDGAGVVALD.VFHVGCFVCSTCRAQLRGQHFYA.ER.RA.C.GCYVAT.EKCAT
Retrocopy	WEYFGQCGGCG-DVVGDGAGVVALDCVFHVGCFVCSTCRAQLRGQHFYAMER<RACCQGCYVATREKCAT

Parental	CSQPILDRILRAMGKAYHPGCFT
	CSQP.LDRILRAMGK.YHP.CFT
Retrocopy	CSQPTLDRILRAMGKDYHPSCFT

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_mmul_2377