RetrogeneDB - Retrocopy retro_mmus

						
>retro_mmus_2438
CTCAGTTCTCCAAGCTATGATTGGTTCCAAACAGAGTCTTCAGTCACCATTGTGGTATACACCAAACAAAAGAATATCAG

TTTAGACTCAGTAATCGTTGACCTCCAGGATGACTCCTCGAGAGCAGACGCAGTCATCAAGGATCATTCTTACCTTGTAC

ATGTTGGGCTAAGCCATGAAGTTCAAGAAAATTTTTCTGTACGGGTTATTGAAAATGTTGGAAAAATAGAGATTGTCCTA

CAAAAGAAAGAAAGTGTTTCTTGGCAATGTCTTGGTGATCACCTGGAGAAACATGATCCTTTCATTCCAAAGAAAGATAC

AGGCTTGTACTACAGACGGTGCCAGTTAATATCTAAGGAAGATGTCACTCATGACACGAGACTTTTCTGTCTGATGCTGC

CTCCAAGTACTCACCTTCAGGTGCCAGTTGGACAACACGTTTACCTCAAGCTCAGTGTCACAGGTGCAGAAATAGTAAAG

CCATATACACCCGTGTCTGATTCCTTACTCTCAGATTTTAAAGAACCAGTTCTTTCCCCAAATAAATACATCTACTTTTT

GATCAAAATCTATCCTGCTGGACTCTTCACACCAGAGCTTGATCGTCTTCAGATTGGAGATTTTATTTCTGTAAGCGGAC

CTGAAGGCAATTTTAAAGTATCCAAACTCCAGGAAGTAGAAGATCTCTTTCTATTGGCAGCCGGAACAGGATTCACACCA

ATGGTCACTGTATTGAATTATGCTTTGTCTCACATGTCCAGTCTCAGGAAGGTGAAGTTGATGTTCTTCAATAAAACAGA

GGACGATATAATTTGGAGATGTCAGCTAGAGAAGTTGGCATTAAGAGAAAAAAGATTTGATGTTGAATTTGTTCTCCCGG

CACCTTCTCTAGAATGGAATTGCAAACAGGGACACATATCACGAGCTCTTCTCTCTGAATTTTTGCAAAGAAGTTCAGAA

AACTCTAGGGCCTTCCTTTGCATCTGCGGACCAACACCATTTACTGACGAGGGGATAAGGTTGATGCATGATCTTAACTT

TTCTGATGATGAGGTTCACGGATTCACCGCT

ORF - retro_mmus_2438 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	97.2 %
Parental protein coverage:	67.61 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalLSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDSLRAEAVIKDHSYLVHVGLSHEVQENFSVRVI
		LSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDS.RA.AVIKDHSYLVHVGLSHEVQENFSVRVI
RetrocopyLSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDSSRADAVIKDHSYLVHVGLSHEVQENFSVRVI
ParentalENVGKIEIVLQKKESVSWQCLGDHLEKHDSFIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ
		ENVGKIEIVLQKKESVSWQCLGDHLEKHD.FIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ
RetrocopyENVGKIEIVLQKKESVSWQCLGDHLEKHDPFIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ
ParentalVPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYICFLIKIYPAGLFTPELDRLQIGDFIS
		VPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYI.FLIKIYPAGLFTPELDRLQIGDFIS
RetrocopyVPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYIYFLIKIYPAGLFTPELDRLQIGDFIS
ParentalVSGPEGDFKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA
		VSGPEG.FKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA
RetrocopyVSGPEGNFKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA
ParentalLREKRFDVEFVLSAPSPEWNGKQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRLLHDLNFSDD
		LREKRFDVEFVL.APS.EWN.KQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRL.HDLNFSDD
RetrocopyLREKRFDVEFVLPAPSLEWNCKQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRLMHDLNFSDD
ParentalEIHGFTA
		E.HGFTA
RetrocopyEVHGFTA

							

							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 .98 RPM	22 .36 RPM
SRP007412_cerebellum	1 .91 RPM	21 .15 RPM
SRP007412_heart	0 .03 RPM	17 .34 RPM
SRP007412_kidney	1 .75 RPM	27 .66 RPM
SRP007412_liver	0 .87 RPM	16 .39 RPM
SRP007412_testis	2 .10 RPM	25 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_2438 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_2438 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_2438 retrocopy 5' end.

Lab - click to see more details

retro_mmus_2438 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_2438 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000010379	1 retrocopy	retro_mluc_448,
Mus musculus	ENSMUSG00000032872	1 retrocopy	retro_mmus_2438 ,

	RetrogeneDB ID:	retro_mmus_2438
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	4:18844204..18845275(-)
	Located in intron of:	ENSMUSG00000087402
Retrocopy information	Ensembl ID:	ENSMUSG00000050550
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	Cyb5r4
	Ensembl ID:	ENSMUSG00000032872
	Aliases:	Cyb5r4, 2810034J18Rik, B5+B5R, C79736, Cb5cb5r, Ncb5or, b5/b5r, b5b5r
	Description:	cytochrome b5 reductase 4 [Source:MGI Symbol;Acc:MGI:2386848]

Parental	LSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDSLRAEAVIKDHSYLVHVGLSHEVQENFSVRVI
	LSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDS.RA.AVIKDHSYLVHVGLSHEVQENFSVRVI
Retrocopy	LSSPSYDWFQTESSVTIVVYTKQKNISLDSVIVDLQDDSSRADAVIKDHSYLVHVGLSHEVQENFSVRVI

Parental	ENVGKIEIVLQKKESVSWQCLGDHLEKHDSFIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ
	ENVGKIEIVLQKKESVSWQCLGDHLEKHD.FIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ
Retrocopy	ENVGKIEIVLQKKESVSWQCLGDHLEKHDPFIPKKDTGLYYRRCQLISKEDVTHDTRLFCLMLPPSTHLQ

Parental	VPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYICFLIKIYPAGLFTPELDRLQIGDFIS
	VPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYI.FLIKIYPAGLFTPELDRLQIGDFIS
Retrocopy	VPVGQHVYLKLSVTGAEIVKPYTPVSDSLLSDFKEPVLSPNKYIYFLIKIYPAGLFTPELDRLQIGDFIS

Parental	VSGPEGDFKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA
	VSGPEG.FKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA
Retrocopy	VSGPEGNFKVSKLQEVEDLFLLAAGTGFTPMVTVLNYALSHMSSLRKVKLMFFNKTEDDIIWRCQLEKLA

Parental	LREKRFDVEFVLSAPSPEWNGKQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRLLHDLNFSDD
	LREKRFDVEFVL.APS.EWN.KQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRL.HDLNFSDD
Retrocopy	LREKRFDVEFVLPAPSLEWNCKQGHISRALLSEFLQRSSENSRAFLCICGPTPFTDEGIRLMHDLNFSDD

Parental	EIHGFTA
	E.HGFTA
Retrocopy	EVHGFTA

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

RetrogeneDB ID:

retro_mmus_2438