RetrogeneDB ID: retro_mmus_2883

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:136486124..136487186(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000091408
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Coq2
• Ensembl ID: ENSMUSG00000029319
• Aliases: Coq2, 2310002F18Rik
• Description: coenzyme Q2 homolog, prenyltransferase (yeast) [Source:MGI Symbol;Acc:MGI:1919133]

Sequence

>retro_mmus_2883
CGGGGCCTGCGGGCCGTTGGGTCCGCATGGCTGCGAGGTTCGCGCGGACTCCCATTGGCCCTGGTGCGCGATCGGCGAGC
CCCGGCCCCCGGGACGCAGTGCGGCCGAGCTCTCAGCCTGTCGGCCGCGGCCGTGGTGAACTCGGCGCCCCGCCCGCTGC
AGCCCTACCTGCGCCTCATGCGCCTGGACAAGCCCATCAGAACCTGGCTGCTGTATTTGCCATGCACTTGGAGCTTTGGT
CTGGCCGCTGACCCAGGTTGTTTTCCAGACATGTTATCACTTTTTTGCACTGGAGCTATTCTGATGCGTGGAGCAGGCTG
TACTATTAATGACATGTGGGACCGTGACTTCGATAAAAAGGTTACAAGGACAGCAAGTCGCCCAATTGCTGCTGGAGACA
TTTCAACCTTCCAGTCCTTTGTCTTCCTTGGGGGACAGCTGACCTTGGCACTGGGCGTTCTCCTGTGTTTAAACTACTAC
AGTATAGCAATGGGAGCAGCGTCCTTACTTCTTGTCATCACCTACCCACTAATGAAAAGAATCACGTTTTGGCCTCAGTT
GGCTTTGGGATTGACTTTTAATTGGGGTGTGTTACTCGGATGGTCTGCTGTCAAGGGCTCCTGTGATCCAGCTGTATGCC
TGCCTCTGTATTTTTCTGGAGTTATGTGGACACTGATATATGATACTATCTATGCCCACCAGGACAAGAAAGACGATGCT
CTGATTGGCCTGAAGTCCACAGCACTGCTGTTTCAGGAGAACACCAGGCAGTGGCTTAGTGGCTTTGGGGTTGCCATGGT
GGCAGCACTGAGCCTGGCTGGAGCCAACAATGGTCAGACCGTCCCCTACTATGCTGCTGTGGCTGCAGTGGGAGCCCACC
TGGCTCACCAGATTTACACTGTAGACATCCACAGAGCCGAGGACTGCTGGGCCAAGTTCACCTCCAACCGCACAGTAGGA
ATGTTCCTGTTCTTAGGGATTGTCCTTGGAAACCTGTGCAAAGAAAAGACAGAAGAAGCAAAAGATGCTGAAGCCGTTAG
AGTGGGAAGTGAGCAGACGAGC

Alignment

ORF - retro_mmus_2883 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.98 %
• Parental protein coverage: 94.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGPRGLPLALVR-SAGVPGA--RDRRAPAPGTQRGRALSLSAAAVVNSAPRPLQPYLRLMRLDKPIGTWL
          RG.R....A..R.S.G.P.A..RDRRAPAPGTQ.GRALSLSAAAVVNSAPRPLQPYLRLMRLDKPI.TWL
Retrocopy RGLRAVGSAWLRGSRGLPLALVRDRRAPAPGTQCGRALSLSAAAVVNSAPRPLQPYLRLMRLDKPIRTWL

Parental  LYLPCTWSIGLAADPGCFPDWYMLSLFGTGAILMRGAGCTINDMWDRDFDKKVTRTANRPIAAGDISTFQ
          LYLPCTWS.GLAADPGCFPD..MLSLF.TGAILMRGAGCTINDMWDRDFDKKVTRTA.RPIAAGDISTFQ
Retrocopy LYLPCTWSFGLAADPGCFPD--MLSLFCTGAILMRGAGCTINDMWDRDFDKKVTRTASRPIAAGDISTFQ

Parental  SFVFLGGQLTLALGVLLCLNYYSIAMGAASLLLVVTYPLVKRITFWPQLALGLTFNWGALLGWSAVKGSC
          SFVFLGGQLTLALGVLLCLNYYSIAMGAASLLLV.TYPL.KRITFWPQLALGLTFNWG.LLGWSAVKGSC
Retrocopy SFVFLGGQLTLALGVLLCLNYYSIAMGAASLLLVITYPLMKRITFWPQLALGLTFNWGVLLGWSAVKGSC

Parental  DPAVCLPLYFSGVMWTLIYDTIYAHQDKKDDALIGLKSTALLFQENTRQWLSGFGVAMVAALSLAGANNG
          DPAVCLPLYFSGVMWTLIYDTIYAHQDKKDDALIGLKSTALLFQENTRQWLSGFGVAMVAALSLAGANNG
Retrocopy DPAVCLPLYFSGVMWTLIYDTIYAHQDKKDDALIGLKSTALLFQENTRQWLSGFGVAMVAALSLAGANNG

Parental  QTVPYYAAVAAVGAHLAHQIYTVDIHRAEDCWDKFTSNRTVGMLLFLGIVLGNLCKEKTEEAKDAEAVRV
          QTVPYYAAVAAVGAHLAHQIYTVDIHRAEDCW.KFTSNRTVGM.LFLGIVLGNLCKEKTEEAKDAEAVRV
Retrocopy QTVPYYAAVAAVGAHLAHQIYTVDIHRAEDCWAKFTSNRTVGMFLFLGIVLGNLCKEKTEEAKDAEAVRV

Parental  GSEQTS
          GSEQTS
Retrocopy GSEQTS

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	0.12 RPM	46.94 RPM
SRP007412_cerebellum	0.35 RPM	25.10 RPM
SRP007412_heart	0.19 RPM	64.81 RPM
SRP007412_kidney	0.65 RPM	41.96 RPM
SRP007412_liver	0.25 RPM	21.82 RPM
SRP007412_testis	0.32 RPM	5.76 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2883 was not detected

EST

No EST(s) were mapped for retro_mmus_2883 retrocopy.

TSS

No TSS is located nearby retro_mmus_2883 retrocopy 5' end.

Lab

retro_mmus_2883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005006	1 retrocopy	retro_amel_1898,
Bos taurus	ENSBTAG00000005744	1 retrocopy	retro_btau_1835,
Cavia porcellus	ENSCPOG00000011458	1 retrocopy	retro_cpor_1202,
Equus caballus	ENSECAG00000012542	1 retrocopy	retro_ecab_432,
Myotis lucifugus	ENSMLUG00000015267	1 retrocopy	retro_mluc_1776,
Mus musculus	ENSMUSG00000029319	1 retrocopy	retro_mmus_2883 ,
Tarsius syrichta	ENSTSYG00000013801	30 retrocopies	retro_tsyr_1015, retro_tsyr_1155, retro_tsyr_1173, retro_tsyr_1180, retro_tsyr_1207, retro_tsyr_1235, retro_tsyr_1327, retro_tsyr_1335, retro_tsyr_1385, retro_tsyr_1451, retro_tsyr_1491, retro_tsyr_1646, retro_tsyr_1709, retro_tsyr_1742, retro_tsyr_2015, retro_tsyr_2062, retro_tsyr_2087, retro_tsyr_2136, retro_tsyr_2146, retro_tsyr_466, retro_tsyr_513, retro_tsyr_533, retro_tsyr_54, retro_tsyr_548, retro_tsyr_607, retro_tsyr_619, retro_tsyr_654, retro_tsyr_776, retro_tsyr_839, retro_tsyr_995,
Tursiops truncatus	ENSTTRG00000005647	1 retrocopy	retro_ttru_1726,