RetrogeneDB ID: retro_mmus_2510

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:119519128..119519865(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080773
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ccnh
• Ensembl ID: ENSMUSG00000021548
• Aliases: Ccnh, 6330408H09Rik, AI661354, AV102684, AW538719
• Description: cyclin H [Source:MGI Symbol;Acc:MGI:1913921]

Sequence

>retro_mmus_2510
TCTGTTGTGAGTACAGCTTGTACGTATTTTAAGCGTTTTTATCTTAATAACTCAGTAATGGAATGTCACCCTTGGATAAT
AACACTAACTTGTGCATTTTTGGCCTGCAAAGTAGATGAATTCAGTGTGTCTAGTCCTCGGTTTGTTGGAAATCTTCGAG
AGAGTCCTCTTGGACAGGAGAGGGCACTGGCACAGATTTTGGAACATGAACTACTACTTATACAACAACTTAATTCCCAC
CTTATTGTCCACAATCCATATAGACCATCGAAGGCTTCTTCATCAATATAAAGACTCGATACCCCATGTTGGAGAATCCG
GCGATATTGAGGAAAACAGCTGATGATTTTCTTAGTAGAATTGCGTTGATAGATGCTTATCTTTTATACACACCTTCACA
AATTGCCCTGACTGCCATTTTATCAAGTGCCTCTAGAGCTGGAATTACTATGGAAAGCTATTTATCAGAGAGTCTAATGC
TGAAAGGAAAGAGAATTTGCCTGTCACAGTTACTGGATATAATGAGAAGCATGAGAAACCTAGTAAAAAAGTATGAGCCA
CCCAGGTCTGAAAAGGTTGCTGTTCTGAGACAGAAGTTAGAGCGATGTCATTCTTCTGACCTTGAACTTAATGTGTTTGT
GAAGAAGAGGAAAGGCTATGAAGATGATGGCTGTGTAGCAAAGAAACCCAAACAGGAAGAGGTGGAATAGACTAATGGTG
ACCTGGTAGACTCTCTT

Alignment

ORF - retro_mmus_2510 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.23 %
• Parental protein coverage: 76.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVVGTACMYFKRFYLNNSVMEYHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQERALEQILEYE
          SVV.TAC.YFKRFYLNNSVME.HP.II.LTCAFLACKVDEF.VSSP.FVGNLRESPLGQERAL.QILE.E
Retrocopy SVVSTACTYFKRFYLNNSVMECHPWIITLTCAFLACKVDEFSVSSPRFVGNLRESPLGQERALAQILEHE

Parental  LLLIQQLNFHLIVHNPYRP-FEGFLIDIKTRYPMLENPEILRKTADDFLSRIALTDAYLLYTPSQIALTA
          LLLIQQLN.HLIVHNPYRP..EGF.I.IKTRYPMLENP.ILRKTADDFLSRIAL.DAYLLYTPSQIALTA
Retrocopy LLLIQQLNSHLIVHNPYRP<IEGFFINIKTRYPMLENPAILRKTADDFLSRIALIDAYLLYTPSQIALTA

Parental  ILSSASRAGITMESYLSESLMLKENRTCLSQLLDIMKSMRNLVKKYEPPRSDEVAVLKQKLERCHSSDLA
          ILSSASRAGITMESYLSESLMLK..R.CLSQLLDIM.SMRNLVKKYEPPRS..VAVL.QKLERCHSSDL.
Retrocopy ILSSASRAGITMESYLSESLMLKGKRICLSQLLDIMRSMRNLVKKYEPPRSEKVAVLRQKLERCHSSDLE

Parental  LNAVTKKRKGYEDDDYVSKKPKQEEEEWTDDDLVDSL
          LN...KKRKGYEDD..V.KKPKQEE.E.T..DLVDSL
Retrocopy LNVFVKKRKGYEDDGCVAKKPKQEEVE*TNGDLVDSL

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	31.91 RPM
SRP007412_cerebellum	0.00 RPM	21.36 RPM
SRP007412_heart	0.00 RPM	15.53 RPM
SRP007412_kidney	0.13 RPM	15.26 RPM
SRP007412_liver	0.00 RPM	10.24 RPM
SRP007412_testis	0.00 RPM	12.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2510 was not detected

EST

No EST(s) were mapped for retro_mmus_2510 retrocopy.

TSS

No TSS is located nearby retro_mmus_2510 retrocopy 5' end.

Lab

retro_mmus_2510 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2510 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510 ,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,