RetrogeneDB ID: retro_mmus_2364

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:75324500..75325677(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083224
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2364
ATGTTGGGACCCATGCCAAGCAGGGCCAGAGTTTACACAGATGTTAACATGCACAGACCCCGAGAGTACTGGGACTGTGA
ATCACATGTGATGGAATGGGGAAATCAAGATGACTACCAGCTTGTTCGAAAATTAGGCAGGGGCAAATACAATGAAGTAT
TTGAAGCCATCAACATCACAAATAATGAAATACGTTATTAAAATCCTCAAGCCAGTAAAAAAAGAAGAGAATTAATCATG
AAATAAAGACTTTGGAGAATCTGAGAAGTGGTCCCAACATCATCACACTTGCAGACATTGTAAAAGGCCTTGTGTCACAA
CCCCCCTGCCTTGGTTTTTGAACATGTAAACAGCACAGACTTCAAGCAATTGTACCAGATGTTAACAGACCGTGACATTC
GATTTTACATGTATGAAATTCTAAAAGCCCTGGATTCTTGTCACAGCAGAGGGATTATGCACAGAGATGTGAAATCCCAT
AACGTCATGATTGATCATGAGCACAGAAAGCTTTGGCTAATAGACTAGAGTTTAGCTGAGTTTTACTGTCCTGGCCAAGA
GTATAATGTCCGAGTTGCTTCCCGATATTTAAAAGATCCAGAGCTACTTGTAGATTATCAGATGTACGATTATAGTTTGG
ATATGTGGGAGTTTGGGTTGTATGCTGGCAAGTATGATCTTCCAGAAGGAGTCATCTTCCCGAGGACATGACAATTATGA
TCAGTTGGTGAGGATAGCCAAGGTTCTGGGGACAGAAGATTTGTATAACTACATTAACAAGTACAATATTGAATTAGATC
CATGTTTCAACAATATCTTGGGCAGACACTCCCAGAAGTGATGGGAATTCTTTGTCCACAGTGAAAACCAGCATCTTGTA
AGCCCCGAGGCCTTGGATTTTGTGTACAAGCTGCTGCAATAAGACCACCAGTTACAGCTCGCTGGAAGAGAGGTCATGGA
ACACCCGTACTTCTACTCTGTTGTGAAGGATAAGGCATGAATGAGTTCCACTAGCATGGCAGGAGGCATCACACCTGTCA
GCAGGGTGAATATGATATCAGGGATTTCTTCAGTGCCAACCCTTTCACCACCTCTTAGACCTCTGGAAGGCTCACCGGTG
AGTGCTGCTCTCAACTCACTTGGGATACATGTTCCAGCTGCTGCTGGAGCTCAGCAA

Alignment

ORF - retro_mmus_2364 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNE-KVVVKI
          M.GP.PSRARVYTDVN.HRPREYWD.ESHV.EWGNQDDYQLVRKLGRGKY.EVFEAINITNNE.....K.
Retrocopy MLGPMPSRARVYTDVNMHRPREYWDCESHVMEWGNQDDYQLVRKLGRGKYNEVFEAINITNNE<NTLLKS

Parental  LKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSR-TPALVFEHVNNTDFKQLYQTLTDYDIRFYMY
          ....KKK.I..EIK.LENLR.GPNIITLADIVK..VS...PALVFEHVN.TDFKQLYQ.LTD.DIRFYMY
Retrocopy SSQ*KKKRINHEIKTLENLRSGPNIITLADIVKGLVSQ>PPALVFEHVNSTDFKQLYQMLTDRDIRFYMY

Parental  EILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQM
          EILKALD.CHS.GIMHRDVK.HNVMIDHEHRKL.LID..LAEFY.PGQEYNVRVASRY.K.PELLVDYQM
Retrocopy EILKALDSCHSRGIMHRDVKSHNVMIDHEHRKLWLID*SLAEFYCPGQEYNVRVASRYLKDPELLVDYQM

Parental  YDYSLDMW-SLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHS
          YDYSLDMW.SLGCMLASMIF.KE....GHDNYDQLVRIAKVLGTEDLY.YI.KYNIELDP.FN.ILGRHS
Retrocopy YDYSLDMW>SLGCMLASMIFQKESSSRGHDNYDQLVRIAKVLGTEDLYNYINKYNIELDPCFNNILGRHS

Parental  RKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMSSTSMAGGSTPVS
          .K.WE.FVHSENQHLVSPEALDF..KLL..DHQ..L..RE.MEHPYFY.VVKD.A.MSSTSMAGG.TPVS
Retrocopy QK*WEFFVHSENQHLVSPEALDFVYKLLQ*DHQLQLAGREVMEHPYFYSVVKDKA*MSSTSMAGGITPVS

Parental  SANMMSGISSVPTPS-PLGPLAGSPVIAAANSLGIPVPAAAGAQQ
          ..NM.SGISSVPT.S.PL.PL.GSPV.AA.NSLGI.VPAAAGAQQ
Retrocopy RVNMISGISSVPTLSPPLRPLEGSPVSAALNSLGIHVPAAAGAQQ

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	0.00 RPM	55.71 RPM
SRP007412_heart	0.00 RPM	64.19 RPM
SRP007412_kidney	0.04 RPM	63.31 RPM
SRP007412_liver	0.00 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_2364 was not detected

EST

No EST(s) were mapped for retro_mmus_2364 retrocopy.

TSS

No TSS is located nearby retro_mmus_2364 retrocopy 5' end.

Lab

retro_mmus_2364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2364 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,