RetrogeneDB ID: retro_mmus_1177

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:14197627..14198464(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Csnk2a1
• Ensembl ID: ENSMUSG00000074698
• Aliases: Csnk2a1, Csnk2a1-rs4
• Description: casein kinase 2, alpha 1 polypeptide [Source:MGI Symbol;Acc:MGI:88543]

Sequence

>retro_mmus_1177
GTCTTTGAACATGGAAACAACACAGAATTCAAGCAATTGTACCAGACGTTAACAGACTATGACATTCGCTTTTACATGTA
TGACATTCTGAAAGCCCTGGATTATTGTCACAGCATGGGGATTATGCACAGAGATGTGAAACCCCATAATGGCACGATTG
ATCATGAGCACAGAAAGCTTCGGCTCATAGACTGGGGTTTAGCTGAGTTTTACCATCCAGGCCAAGAGTATAATGTCCGA
GTTGCTTCTTGATATTTCAAAGGTCCAGAGCTACTTGTAGATTATCAGATGTATGATTATAGTTTGGATATGTGGATCTT
GGGTTGTATGCTGGCCAGTATGATCTTCTGGAAGGAGCCATTTTTTCCATGGACATGACAATTATGATCAGTTGGTGAGG
AGAGCCAAGGTTCTGGGAACAGAAGATTTATATGACTATATTGACAAGTACAACATTGAATTAGATCCACATTTCAACGA
TATCTTGGGCAGACACTCCGGTAAGCGATGGGAACGCTTTGTCCACAGTGAAAACCAGCATCTTGTCAGCCCTGAGGCCT
TGGATTTTCTGGACAAGCTGCTGCTATACGACCAACAGTCACGGCTCACTGCAAGAGAGGCCATGGAGCACCCTTACTTC
ACTGTTGTGAAGGACCAGGCTCGAATGAGTTCCACTAGCATGGTAGGGGCAGCACACATGTCAGCAGTGCCAATATGACA
TCAGCGATTTCTTCAATGCCAACCCCTTCACCCCTTGGACCTCTGGCAGGCTCACCAGTGATTGTTGCTGCCAACTCACT
TGGGATACCTGTTCCAACTGCTGCTGGCGCTCAGCAG

Alignment

ORF - retro_mmus_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.84 %
• Parental protein coverage: 71.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEF
          VFEH.NNT.FKQLYQTLTDYDIRFYMY.ILKALDYCHSMGIMHRDVKPHN..IDHEHRKLRLIDWGLAEF
Retrocopy VFEHGNNTEFKQLYQTLTDYDIRFYMYDILKALDYCHSMGIMHRDVKPHNGTIDHEHRKLRLIDWGLAEF

Parental  YHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEP-FFHGHDNYDQLVRIAKVLG
          YHPGQEYNVRVAS.YFKGPELLVDYQMYDYSLDMW.LGCMLASMIF.KEP.FFHGHDNYDQLVR.AKVLG
Retrocopy YHPGQEYNVRVAS*YFKGPELLVDYQMYDYSLDMWILGCMLASMIFWKEP>FFHGHDNYDQLVRRAKVLG

Parental  TEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAME
          TEDLYDYIDKYNIELDP.FNDILGRHS.KRWERFVHSENQHLVSPEALDFLDKLL.YD.QSRLTAREAME
Retrocopy TEDLYDYIDKYNIELDPHFNDILGRHSGKRWERFVHSENQHLVSPEALDFLDKLLLYDQQSRLTAREAME

Parental  HPYFYTVVKDQARMSSTSMAG-GSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANSLGIPVPAAAGA
          HPYF.TVVKDQARMSSTSM.G.GST.VSSANM.S.ISS.PTPSPLGPLAGSPVI.AANSLGIPVP.AAGA
Retrocopy HPYF-TVVKDQARMSSTSMVG<GSTHVSSANMTSAISSMPTPSPLGPLAGSPVIVAANSLGIPVPTAAGA

Parental  QQ
          QQ
Retrocopy QQ

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	57.75 RPM
SRP007412_cerebellum	0.04 RPM	55.71 RPM
SRP007412_heart	0.03 RPM	64.19 RPM
SRP007412_kidney	0.00 RPM	63.31 RPM
SRP007412_liver	0.03 RPM	54.15 RPM
SRP007412_testis	0.00 RPM	12.67 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1177 was not detected

EST

No EST(s) were mapped for retro_mmus_1177 retrocopy.

TSS

No TSS is located nearby retro_mmus_1177 retrocopy 5' end.

Lab

retro_mmus_1177 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1177 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006946	1 retrocopy	retro_cfam_1408,
Homo sapiens	ENSG00000101266	1 retrocopy	retro_hsap_53,
Mus musculus	ENSMUSG00000074698	3 retrocopies	retro_mmus_1177 , retro_mmus_2364, retro_mmus_377,
Otolemur garnettii	ENSOGAG00000002709	1 retrocopy	retro_ogar_820,