RetrogeneDB ID: retro_mmus_3643

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:77290246..77290815(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084202
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ctsh
• Ensembl ID: ENSMUSG00000032359
• Aliases: Ctsh, AL022844
• Description: cathepsin H [Source:MGI Symbol;Acc:MGI:107285]

Sequence

>retro_mmus_3643
ATGTGCGCTGCGCTGCCACCACTCTGGACAGGGCCTGGCTGCTGAGAATGCAGGCCAACGCTGAGCTGACAGTCAACGCC
ACAGAAAAATTTCACTTTAAGTCATGGACAAAACAGCATCAAAAGACGTACAGCTTAGAGGAGTAAAACCATAGGCTGCA
GATGTTTGCCAACAACTGGAGGAAGATTCATGACCACAACCAGAGGAACCACACATTTAAATTTGTGTTGAACCAGTTTT
CAGATATGAGCTTTGCTGAAATAAAACACAAATATTTCTGGTCAGAGCCTCAGAACTGCTCAGCCACCAAAAGTAACTGT
CTCCGTGGTACTGGCCCCTACCCTGCCTCCGTGGAATGTCTGAAGAAAGGAAGTGTTGTTTTAGCAGGGAAAAATCAGGG
GGCCTGTGGCAGTTTCTGGACTTTCTCCATCACGGAGGCCCTAGGGTCGGCTGTGGCTATTGCCAGTGGGAAAATGCTGT
CTTTGGCTGAACAGCAGCTGGTGGATTGTGCCCAGGACAATCATGGCAGCGAAGGAGGTCTCCCCAGCCAGACCTTCGAG
TACATCCTG

Alignment

ORF - retro_mmus_3643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 57.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MWAALPLLCAG-AWLLSTGATAELTVNAIEKFHFKSWMKQHQKTYSSVEYNHRLQMFANNWRKIQAHNQR
          M.AALP.L..G.AWLL...A.AELTVNA.EKFHFKSW.KQHQKTYS..E.NHRLQMFANNWRKI..HNQR
Retrocopy MCAALPPLWTG<AWLLRMQANAELTVNATEKFHFKSWTKQHQKTYSLEE*NHRLQMFANNWRKIHDHNQR

Parental  NHTFKMALNQFSDMSFAEIKHKFLWSEPQNCSATKSNYLRGTGPYPSSMDWRKKGNVVSPVKNQGACGSC
          NHTFK..LNQFSDMSFAEIKHK..WSEPQNCSATKSN.LRGTGPYP.S....KKG.VV...KNQGACGS.
Retrocopy NHTFKFVLNQFSDMSFAEIKHKYFWSEPQNCSATKSNCLRGTGPYPASVECLKKGSVVLAGKNQGACGSF

Parental  WTFSTTGALESAVAIASGKMLSLAEQQLVDCAQAFNNHGCKGGLPSQAFEYIL
          WTFS.T.AL.SAVAIASGKMLSLAEQQLVDCAQ...NHG..GGLPSQ.FEYIL
Retrocopy WTFSITEALGSAVAIASGKMLSLAEQQLVDCAQ--DNHGSEGGLPSQTFEYIL

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	0.23 RPM	8.50 RPM
SRP007412_cerebellum	0.13 RPM	6.51 RPM
SRP007412_heart	0.00 RPM	26.90 RPM
SRP007412_kidney	0.02 RPM	102.99 RPM
SRP007412_liver	0.00 RPM	200.50 RPM
SRP007412_testis	0.09 RPM	5.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3643 was not detected

EST

No EST(s) were mapped for retro_mmus_3643 retrocopy.

TSS

No TSS is located nearby retro_mmus_3643 retrocopy 5' end.

Lab

retro_mmus_3643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3643 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021939	1 retrocopy	retro_mmus_1921,
Mus musculus	ENSMUSG00000032359	1 retrocopy	retro_mmus_3643 ,