RetrogeneDB ID: retro_mmus_1200

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:51359247..51359964(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cdk8
• Ensembl ID: ENSMUSG00000029635
• Aliases: None
• Description: cyclin-dependent kinase 8 [Source:MGI Symbol;Acc:MGI:1196224]

Sequence

>retro_mmus_1200
GAACTACTAACGTCAGAACCAATATTTTATTGTCGACAAGAGGACATCAAAACTAGTAATCCTTATCACCATGACCAGCT
GGACAGAATATTCAATGTAATGGGATTCCCTGCAGATAAAGATTGGGAAGATATAAAAAAGATGCCTGAACATTCAACAT
TAATGAAAGATTTCAGAAGAAATACGTATACCAATTGCAGCCTTATCAAGTATATGGAAAAGCATAAAGTTAAACCCGAT
AGTAAAGCATTCCATTTGCTTCAGAAGTTGCTCACTATGGACCCAATACAGCGAATTACCTCAGAGCAGGCCATGCAGGA
CCCCTACTTCCTAGAAGACCCACTTCCCACGTCAGATGTTTTCGCCGGTTGTCAGATCCCGTATCCCAAATGAGAATTTT
TAACAGAAGAAGAGCCTGATGAGAAAGGAGACAAAAAGACCCAGCAGCAGCAGCAGGGCAACAACCACACTAACGGAACT
GGCCATCCAGGGAACCAGGACAGCGGCCACGCACAAGGGCCCCCCTTGAAAAAAGTGAGAGTTCTCCCTCCTACCACTAC
CTCAGGTGGACTCATCATGACCCCCGACTATCAGCGTTCCAATCCACATGCTGCTTATCCCAACCCTGGACCAAGCACAT
CACAGCCCCAGAGCAGCATGGGATACTCAGCTACCTCCCAGCAGCCTCCACAGTACTCACATCAGACATATCGGTAC

Alignment

ORF - retro_mmus_1200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.49 %
• Parental protein coverage: 51.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIK
          ELLTSEPIF.CRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIK
Retrocopy ELLTSEPIFYCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIK

Parental  YMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPD
          YMEKHKVKPDSKAFHLLQKLLTMDPI.RITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPK.EFLTEEEPD
Retrocopy YMEKHKVKPDSKAFHLLQKLLTMDPIQRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPK*EFLTEEEPD

Parental  EKGDKKTQQQQQGNNHTNGTGHPGNQDSGHAQGPPLKKVRVVPPTTTSGGLIMTSDYQRSNPHAAYPNPG
          EKGDKKTQQQQQGNNHTNGTGHPGNQDSGHAQGPPLKKVRV.PPTTTSGGLIMT.DYQRSNPHAAYPNPG
Retrocopy EKGDKKTQQQQQGNNHTNGTGHPGNQDSGHAQGPPLKKVRVLPPTTTSGGLIMTPDYQRSNPHAAYPNPG

Parental  PSTSQPQSSMGYSATSQQPPQYSHQTHRY
          PSTSQPQSSMGYSATSQQPPQYSHQT.RY
Retrocopy PSTSQPQSSMGYSATSQQPPQYSHQTYRY

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	0.09 RPM	19.48 RPM
SRP007412_cerebellum	0.09 RPM	22.19 RPM
SRP007412_heart	0.06 RPM	14.07 RPM
SRP007412_kidney	0.08 RPM	27.80 RPM
SRP007412_liver	0.08 RPM	27.75 RPM
SRP007412_testis	0.09 RPM	17.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1200 was not detected

EST

No EST(s) were mapped for retro_mmus_1200 retrocopy.

TSS

No TSS is located nearby retro_mmus_1200 retrocopy 5' end.

Lab

retro_mmus_1200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001443	1 retrocopy	retro_chof_1102,
Homo sapiens	ENSG00000132964	1 retrocopy	retro_hsap_2147,
Myotis lucifugus	ENSMLUG00000009176	1 retrocopy	retro_mluc_112,
Macaca mulatta	ENSMMUG00000014841	1 retrocopy	retro_mmul_1010,
Mus musculus	ENSMUSG00000029635	1 retrocopy	retro_mmus_1200 ,
Nomascus leucogenys	ENSNLEG00000014010	1 retrocopy	retro_nleu_2746,