RetrogeneDB ID: retro_mmus_593

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:97242172..97242527(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cwc15
• Ensembl ID: ENSMUSG00000004096
• Aliases: Cwc15, 0610040D20Rik, 2900052N06Rik, Ed1, c11orf5, mED1
• Description: CWC15 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913320]

Sequence

>retro_mmus_593
AGGGCCCCTCCTCCCCAAGAACATACAACTTCCTCTTCAGTGTCATGAAACCTCACTTAGCCTTAGACGAGACTCCTGCC
ACCAACCTTGATGCTATTGATCCTCTCACAGATGAGGAAGATGAGGATTTTGAAGAAGAAAGCGATGACTATGCTACTGC
GCCTTTTTGTAGAGCTGAAAAAAAAATCAAGAAGTAAAGAGCTGAATAACAGGCCAGGAAAGAAAAGGAACAAATAGCAG
AGGACTAGAGAATTTGCACGAAAAACATTCTGAATGAAACCTTCTCCATAATCCCAAAGACCCATCCCAGCCTCAGCGCA
ACCTCAACATTAAAAGAAGGTAGGAAGATGATGTC

Alignment

ORF - retro_mmus_593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.16 %
• Parental protein coverage: 51.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RDRPTREHTTSSSVS-KKPRL--DQIPAANLDADDPLTDEEDEDFEEESDDDDTAALLAELEKIKKERAE
          R..P..EHTTSSSVS..KP.L..D..PA.NLDA.DPLTDEEDEDFEEESDD..TA.........KK.RAE
Retrocopy RAPPPQEHTTSSSVS<MKPHLALDETPATNLDAIDPLTDEEDEDFEEESDDYATAPFCRAXXXXKK*RAE

Parental  EQARKEQEQKAEEERIRMENILSG-NPLLNLTGPSQPQANFKVKRRWDDDV
          .QARKE.EQ.AE..RI...NIL...N.L.N...PSQPQ.N...KRR..DDV
Retrocopy *QARKEKEQIAED*RICTKNILNE<NLLHNPKDPSQPQRNLNIKRR*EDDV

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	36.40 RPM
SRP007412_cerebellum	0.00 RPM	47.59 RPM
SRP007412_heart	0.00 RPM	37.45 RPM
SRP007412_kidney	0.00 RPM	51.55 RPM
SRP007412_liver	0.00 RPM	44.90 RPM
SRP007412_testis	0.00 RPM	59.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_593 was not detected

EST

No EST(s) were mapped for retro_mmus_593 retrocopy.

TSS

No TSS is located nearby retro_mmus_593 retrocopy 5' end.

Lab

retro_mmus_593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_593 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2452

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Callithrix jacchus	ENSCJAG00000004188	1 retrocopy	retro_cjac_2802,
Cavia porcellus	ENSCPOG00000006249	1 retrocopy	retro_cpor_708,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Mus musculus	ENSMUSG00000004096	2 retrocopies	retro_mmus_2482, retro_mmus_593 ,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Otolemur garnettii	ENSOGAG00000001686	2 retrocopies	retro_ogar_2476, retro_ogar_456,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,