RetrogeneDB ID: retro_mmus_3454

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:53418330..53418967(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083798
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Csnk1g3
• Ensembl ID: ENSMUSG00000073563
• Aliases: Csnk1g3, 3300002K07Rik, C330049O21Rik
• Description: casein kinase 1, gamma 3 [Source:MGI Symbol;Acc:MGI:1917675]

Sequence

>retro_mmus_3454
GGTAAATACAACGCGATGGTGCTGGAACTGCTGGGACCGAGTTTGGAGGATTTGTTTGACCTCTGTGATAGAACGTTTTC
TCTTAAAACAGTTCTCATGATAGCTATACAGCTGATTTCTCGTATGGAGTATGTCCACTCAAAGAACTTGATATACAGAG
ATGTGAAGCCTGAGAACTTCTTAATAGGACGGCCGGGAAACAAAGCCCAGCAAGTCATTCATATCATAGATTTTGGTTTG
GCAAAGGAATATATTGATCCAGAGACAAAGAAACATATACCATACAGAGAACACAAAAGCCTTACCGGAACCGCCAGATA
CATGAGCATAAACACACATCTAGGAAAAGAGCAGAGTAGAAGAGATGATTTAGAAGCCTTAGGCCACATGTTCATGTACT
TCCTGAGAGGCAGTCTTCCTTGGCAAGGCTTAAAGGCTGACACATTAAAAGAGAGGTATCAGAAAATTGGAGACACAAAA
CGAGCCACACCAATAGAAGTGTTGTGTGAGAACTTCCCAGAAATGGCAACGTATCTCCGTTACGTACGAAGGCTGGATTT
TTTTTGAAAAGCCAGACTATGATTACCTAAGAAAGCTTTTTACTGACTTGTTTGATCGAAAAGGGTATATGTTTGAT

Alignment

ORF - retro_mmus_3454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.66 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKAQ
          GKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKAQ
Retrocopy GKYNAMVLELLGPSLEDLFDLCDRTFSLKTVLMIAIQLISRMEYVHSKNLIYRDVKPENFLIGRPGNKAQ

Parental  QVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLP
          QVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLP
Retrocopy QVIHIIDFGLAKEYIDPETKKHIPYREHKSLTGTARYMSINTHLGKEQSRRDDLEALGHMFMYFLRGSLP

Parental  WQGLKADTLKERYQKIGDTKRATPIEVLCENFPEEMATYLRYVRRL-DFFEKPDYDYLRKLFTDLFDRKG
          WQGLKADTLKERYQKIGDTKRATPIEVLCENFPE.MATYLRYVRRL....EKPDYDYLRKLFTDLFDRKG
Retrocopy WQGLKADTLKERYQKIGDTKRATPIEVLCENFPE-MATYLRYVRRL>XXXEKPDYDYLRKLFTDLFDRKG

Parental  YMFD
          YMFD
Retrocopy YMFD

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	0.89 RPM	53.31 RPM
SRP007412_cerebellum	1.00 RPM	44.77 RPM
SRP007412_heart	0.16 RPM	12.61 RPM
SRP007412_kidney	1.27 RPM	42.91 RPM
SRP007412_liver	0.87 RPM	38.29 RPM
SRP007412_testis	0.50 RPM	11.80 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3454 was not detected

EST

1 EST(s) were mapped to retro_mmus_3454 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CX214499	53418547	53418663	100	116	0	116

TSS

No TSS is located nearby retro_mmus_3454 retrocopy 5' end.

Lab

retro_mmus_3454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017550	1 retrocopy	retro_btau_1659,
Callithrix jacchus	ENSCJAG00000017348	2 retrocopies	retro_cjac_2695, retro_cjac_3279,
Macaca mulatta	ENSMMUG00000006646	1 retrocopy	retro_mmul_1040,
Mus musculus	ENSMUSG00000002205	1 retrocopy	retro_mmus_915,
Mus musculus	ENSMUSG00000073563	1 retrocopy	retro_mmus_3454 ,
Otolemur garnettii	ENSOGAG00000011587	1 retrocopy	retro_ogar_246,
Rattus norvegicus	ENSRNOG00000016677	1 retrocopy	retro_rnor_2189,