RetrogeneDB ID: retro_mmul_391

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:94642870..94644080(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1931
• Ensembl ID: ENSMMUG00000023469
• Aliases: None
• Description: heat shock protein 90kDa beta (Grp94), member 1 precursor [Source:RefSeq peptide;Acc:NP_001182453]

Sequence

>retro_mmul_391
GAAGATGAATACAAAGCTTTTTACAAATCGTTTTCAAAGAAAAGTGATGACCCCATGGCTTATATTCGCTTTACCGCTGA
AGGGGAAGTTACCTTCAAGTCAGTTTTATTTGTACCCACATCTGCTCCACGTGGTCTATTTGACGAATATGGATCTAAAA
AGAGTGATTACATTAAGCTCTATGTGCACTGTGTATTCATCACAGATAACTTCCGTGATATGATGTCTAAGTACCTTAAT
TTTGTCAAGGGTGTAGTGGACTCAGATGATCTCCCCTTGAATGTTTCTCTTGAGACTCTTCAACAACATAAACTGCTTAA
GGTGATTAGGAAGAAGCTTGTTTGTAAAACTCTGGACATGATCAAGAAGATTGCTGATGAGAAATACAATGATACTTTTT
GGAAAGAATTTGGTACCAACATCAAGCTTGGTGTGACTGAAGACCACTCGAATCAAACACGTCTTGCTAAACTTCTTATG
TTCCAGTCTTCTCATCATCCAACTGACATTACTACCCTAGACCAGTATGTGGAAAGAATGAAGAGAAAACAAGACAAAAT
CTACTTCATGGCTGGGTCCAGCAGAAAAGAGGCTGAATCTTCTCTATGTTTAGCGACTTCTGAAAAAGGGCTATGAAGTT
ATTTACCTCACAGAACCTGTGGATGAATACTGCAGTCAGACCCTTCCCAAATTTGATGGGAAGAGGTTCCAGAATGTTGT
CAAGGAAGGAGTGAAGTTTGATGAAAGTGAGAAAACTAAGGAGAGTTGTGAAACAGTTGAGAAAGAATTTGAGCCTCTGC
TCAATTGGATGAAAGATAAAGCCCTTAAGGACAAAATTGAGAAGGCTGTGGTGTCTCAGCACCTGACAGAATCTCTGTGT
GCTTTGGTGGCCAGTCAGTACGGACTGTCTGGCAACATGGACAGAATCATGAAAGCATAAGCATATCAAACGAGCAAGGA
CAGCTCTACAAATTACTATGCAAGTCAGAAGAAAACATTTGAAATTAATCCTAAACACCCGCTGATCAGAGACATGCTTC
GATGAATTAAGGAAAGGTGAAGATGATAAAATAGTCTTGAATCTTGCTGTGGTTTTGTGTGAAACAGCAATGCTTCGGTC
AGGATATCTTTTACCAGACACTAAAGCATATGGAGATAGAATAGAAAGAATGCTTCCCTAAGTTTGAACATTGACCCTGA
TGCAAAGTTG

Alignment

ORF - retro_mmul_391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 50.25 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EDEYKAFYKSFSKESDDPMAYIHFTAEGEVTFKSILFVPTSAPRGLFDEYGSKKSDYIKLYVRRVFITDD
          EDEYKAFYKSFSK.SDDPMAYI.FTAEGEVTFKS.LFVPTSAPRGLFDEYGSKKSDYIKLYV..VFITD.
Retrocopy EDEYKAFYKSFSKKSDDPMAYIRFTAEGEVTFKSVLFVPTSAPRGLFDEYGSKKSDYIKLYVHCVFITDN

Parental  FHDMMPKYLNFVKGVVDSDDLPLNVSRETLQQHKLLKVIRKKLVRKTLDMIKKIADDKYNDTFWKEFGTN
          F.DMM.KYLNFVKGVVDSDDLPLNVS.ETLQQHKLLKVIRKKLV.KTLDMIKKIAD.KYNDTFWKEFGTN
Retrocopy FRDMMSKYLNFVKGVVDSDDLPLNVSLETLQQHKLLKVIRKKLVCKTLDMIKKIADEKYNDTFWKEFGTN

Parental  IKLGVIEDHSNRTRLAKLLRFQSSHHPTDITSLDQYVERMKEKQDKIYFMAGSSRKEAESSP-FVERLLK
          IKLGV.EDHSN.TRLAKLL.FQSSHHPTDIT.LDQYVERMK.KQDKI......S......S...V.RLLK
Retrocopy IKLGVTEDHSNQTRLAKLLMFQSSHHPTDITTLDQYVERMKRKQDKI-YFMAGSSRKEAESS>YV*RLLK

Parental  KGYEVIYLTEPVDEYCIQALPEFDGKRFQNVAKEGVKFDESEKTKESREAVEKEFEPLLNWMKDKALKDK
          KGYEVIYLTEPVDEYC.Q.LP.FDGKRFQNV.KEGVKFDESEKTKES.E.VEKEFEPLLNWMKDKALKDK
Retrocopy KGYEVIYLTEPVDEYCSQTLPKFDGKRFQNVVKEGVKFDESEKTKESCETVEKEFEPLLNWMKDKALKDK

Parental  IEKAVVSQRLTESPCALVASQYGWSGNMERIMKAQAYQTGKDISTNYYASQKKTFEINPRHPLIRDMLRR
          IEKAVVSQ.LTES.CALVASQYG.SGNM.RIMKA.AYQT.KD.STNYYASQKKTFEINP.HPLIRDMLR.
Retrocopy IEKAVVSQHLTESLCALVASQYGLSGNMDRIMKA*AYQTSKDSSTNYYASQKKTFEINPKHPLIRDMLR*

Parental  IKE-DEDDKTVLDLAVVLFETATLRSGYLLPDTKAYGDRIERML-RLSLNIDPDAKV
          IKE..EDDK.VL.LAVVL.ETA.LRSGYLLPDTKAYGDRIERML..LSLNIDPDAK.
Retrocopy IKE>GEDDKIVLNLAVVLCETAMLRSGYLLPDTKAYGDRIERML<SLSLNIDPDAKL

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	0.11 RPM	292.56 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	194.60 RPM
SRP007412_cerebellum	0.13 RPM	190.11 RPM
SRP007412_heart	0.00 RPM	279.71 RPM
SRP007412_kidney	0.00 RPM	463.37 RPM
SRP007412_liver	0.12 RPM	521.52 RPM
SRP007412_testis	0.08 RPM	517.80 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_391 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_391 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_184
Pan troglodytes	retro_ptro_170

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000166598	2 retrocopies	retro_hsap_1530, retro_hsap_184,
Macaca mulatta	ENSMMUG00000011073	2 retrocopies	retro_mmul_1526, retro_mmul_2313,
Macaca mulatta	ENSMMUG00000022686	2 retrocopies	retro_mmul_1319, retro_mmul_1869,
Macaca mulatta	ENSMMUG00000023469	1 retrocopy	retro_mmul_391 ,
Nomascus leucogenys	ENSNLEG00000006510	1 retrocopy	retro_nleu_993,
Pan troglodytes	ENSPTRG00000005372	1 retrocopy	retro_ptro_170,