RetrogeneDB ID: retro_mmus_2289

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:108451267..108451527(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cyb5b
• Ensembl ID: ENSMUSG00000031924
• Aliases: Cyb5b, 1810044O22Rik, AU015618, Cyb5m
• Description: cytochrome b5 type B [Source:MGI Symbol;Acc:MGI:1913677]

Sequence

>retro_mmus_2289
GAGGTTCTGCTGGAACAAGCTGGTACTGCTGCAGCCGAAAGCTTTGAAGATGTCAGCCACTCCCGTGATGCTAGGGAGAT
GCTAAAGCAGTACTACATTGGTGATGTCCATTCGAGTGACCTTAAACCAAAAGGTGGTAACAAGGATCCTTTAGAAAGCA
AAAATGCCAAAGTAGCTGGGCATACTGGATTGTCCTCATCGTGGGCACTATTCTTATAGGTTTCCCGTGCCATCACTTCT
CAACTGACAGCACATACTCC

Alignment

ORF - retro_mmus_2289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 59.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVLLEQAGADATESFEDVGHSPDAREMLKQYYIGDVHPSDLKPKGDDKDPSKNNS-CQSSWAYWFVPIVG
          EVLLEQAG..A.ESFEDV.HS.DAREMLKQYYIGDVH.SDLKPKG..KDP......CQSSWAYW.V.IVG
Retrocopy EVLLEQAGTAAAESFEDVSHSRDAREMLKQYYIGDVHSSDLKPKGGNKDPLESKN<CQSSWAYWIVLIVG

Parental  AILIGFLYRHFWADSKSS
          .ILIGF...HF..DS..S
Retrocopy TILIGFPCHHFSTDSTYS

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	151.51 RPM
SRP007412_cerebellum	0.00 RPM	113.16 RPM
SRP007412_heart	0.00 RPM	78.26 RPM
SRP007412_kidney	0.00 RPM	410.31 RPM
SRP007412_liver	0.00 RPM	500.24 RPM
SRP007412_testis	0.00 RPM	59.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2289 was not detected

EST

No EST(s) were mapped for retro_mmus_2289 retrocopy.

TSS

No TSS is located nearby retro_mmus_2289 retrocopy 5' end.

Lab

retro_mmus_2289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000007518	1 retrocopy	retro_apla_13,
Cavia porcellus	ENSCPOG00000014234	1 retrocopy	retro_cpor_1117,
Felis catus	ENSFCAG00000024541	1 retrocopy	retro_fcat_1816,
Gallus gallus	ENSGALG00000000660	1 retrocopy	retro_ggal_13,
Meleagris gallopavo	ENSMGAG00000008619	1 retrocopy	retro_mgal_12,
Myotis lucifugus	ENSMLUG00000006608	1 retrocopy	retro_mluc_1734,
Macaca mulatta	ENSMMUG00000012039	1 retrocopy	retro_mmul_128,
Mus musculus	ENSMUSG00000024646	1 retrocopy	retro_mmus_2177,
Mus musculus	ENSMUSG00000031924	1 retrocopy	retro_mmus_2289 ,
Oryctolagus cuniculus	ENSOCUG00000007729	2 retrocopies	retro_ocun_141, retro_ocun_255,
Pteropus vampyrus	ENSPVAG00000015984	1 retrocopy	retro_pvam_977,
Sarcophilus harrisii	ENSSHAG00000014200	1 retrocopy	retro_shar_688,
Ictidomys tridecemlineatus	ENSSTOG00000011316	1 retrocopy	retro_itri_1296,
Tursiops truncatus	ENSTTRG00000010016	1 retrocopy	retro_ttru_521,
Drosophila melanogaster	FBgn0029854	1 retrocopy	retro_dmel_39,