RetrogeneDB ID: retro_mmus_394

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:178266203..178267103(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dppa2
• Ensembl ID: ENSMUSG00000072419
• Aliases: Dppa2, 2410088E07Rik, C80932, D19Mgi18, ECAT15-2
• Description: developmental pluripotency associated 2 [Source:MGI Symbol;Acc:MGI:2157523]

Sequence

>retro_mmus_394
ATGTCATACTTCGGCCTGGAGACTTTCAATGAGAACCTATCTAAGGAAAACTTGGATGAAGAAAGTGTGATTTTAACGCT
GGTCCAATTTAAGGAGGGGGAGCCAATCACAGTCTAACTTACGCAATCAAATGTTTCTTCTTCAACCTTAGACCACACAC
CACCAGCTCGTTCTCTGGTGAGGCATGCGGGAATCAAACACCCAACCAGAACCATACCAAGCACCTGTCCTCTGCCCAGC
CTGCCTCCTATTAGGGACGTGTCCCGGAACACTCTTCGGGAGTGGTGTCGGTATCATAACTTGAGTACGGATGGCAAGAA
AGTTGAGGTCTATTTGAGACTTCGGAGACACTCCTATTCTAAACAAGAATGTTATATTCCCAATACATCTCGGGAGGCCA
GAATGAAGCAGGGTCCCAAGAAATCCAAGATAGTCTACCGAGGAATCGGGCCTCCAAGCAGGTGCCAAAGGAGAAAGGAG
GAGAGTGGTGTCCTGGAAATTCTAACTTCACCTAAGGAGTCCACATTTGCAGCCTGGGCAAGGATTGCCATGAGAGCAGC
TCAGTCAATGTCTAAGAATCGATGTCCTCTTCCGTCTAATGTGGAGGCCTTTCTGCCACAAGCCACTGGATCCAGATGGT
GTGTTGTCCATGGCAGGCAGCTTCCTGCAGATAAGAAAGGCTGGGTTCGCCTGCAATTTCTTGCTGGACAGACCTGGGTT
CCAGACACTCCCCAAAGGATGAATTTTCTCTTCCTGTTACCGGCCTGTATTATCCCAGAACCAGGAGTGGAAGATAATTT
GCTATGTCCTGAATGTGTTCACAGCAACAAGAAGATCCTAAGAAACTTTAAAATTAGAAGCCGTGCAAAGAAAAATGCTC
TACCCCCAAATATGCCGCCT

Alignment

ORF - retro_mmus_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYFGLETFNENQSEENLDEESVILTLVPFKEEEEPNTDYATQSNVSSSTLDHTPPARSLVRHAGIKHPT
          MSYFGLETFNEN.S.ENLDEESVILTLV.FKE.E.P.T...TQSNVSSSTLDHTPPARSLVRHAGIKHPT
Retrocopy MSYFGLETFNENLSKENLDEESVILTLVQFKEGE-PITV*LTQSNVSSSTLDHTPPARSLVRHAGIKHPT

Parental  RTIPSTCPPPSLPPIRDVSRNTLREWCRYHNLSTDGKKVEVYLRLRRHSYSKQECYIPNTSREARMKQGP
          RTIPSTCP.PSLPPIRDVSRNTLREWCRYHNLSTDGKKVEVYLRLRRHSYSKQECYIPNTSREARMKQGP
Retrocopy RTIPSTCPLPSLPPIRDVSRNTLREWCRYHNLSTDGKKVEVYLRLRRHSYSKQECYIPNTSREARMKQGP

Parental  KKSKIVFRGIGPPSGCQRKKEESGVLEILTSPKESTFAAWARIAMRAAQSMSKNRCPLPSNVEAFLPQAT
          KKSKIV.RGIGPPS.CQR.KEESGVLEILTSPKESTFAAWARIAMRAAQSMSKNRCPLPSNVEAFLPQAT
Retrocopy KKSKIVYRGIGPPSRCQRRKEESGVLEILTSPKESTFAAWARIAMRAAQSMSKNRCPLPSNVEAFLPQAT

Parental  GSRWCVVHGRQLPADKKGWVRLQFLAGQTWVPDTPQRMNFLFLLPACIIPEPGVEDNLLCPECVHSNKKI
          GSRWCVVHGRQLPADKKGWVRLQFLAGQTWVPDTPQRMNFLFLLPACIIPEPGVEDNLLCPECVHSNKKI
Retrocopy GSRWCVVHGRQLPADKKGWVRLQFLAGQTWVPDTPQRMNFLFLLPACIIPEPGVEDNLLCPECVHSNKKI

Parental  LRNFKIRSRAKKNALPPNMPP
          LRNFKIRSRAKKNALPPNMPP
Retrocopy LRNFKIRSRAKKNALPPNMPP

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	0.00 RPM
SRP007412_cerebellum	0.04 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.05 RPM	0.46 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_394 was not detected

EST

No EST(s) were mapped for retro_mmus_394 retrocopy.

TSS

No TSS is located nearby retro_mmus_394 retrocopy 5' end.

Lab

retro_mmus_394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_394 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 66 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020460	2 retrocopies	retro_btau_435, retro_btau_529,
Callithrix jacchus	ENSCJAG00000020168	4 retrocopies	retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Dasypus novemcinctus	ENSDNOG00000010745	6 retrocopies	retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583, retro_dnov_2656,
Erinaceus europaeus	ENSEEUG00000008944	4 retrocopies	retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi	ENSETEG00000007985	4 retrocopies	retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens	ENSG00000163530	3 retrocopies	retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Microcebus murinus	ENSMICG00000013744	6 retrocopies	retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus	ENSMLUG00000007444	1 retrocopy	retro_mluc_1706,
Macaca mulatta	ENSMMUG00000022112	3 retrocopies	retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mus musculus	ENSMUSG00000058550	3 retrocopies	retro_mmus_1907, retro_mmus_2085, retro_mmus_3656,
Mus musculus	ENSMUSG00000072419	7 retrocopies	retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394 ,
Nomascus leucogenys	ENSNLEG00000004020	2 retrocopies	retro_nleu_1329, retro_nleu_633,
Oryctolagus cuniculus	ENSOCUG00000003175	1 retrocopy	retro_ocun_61,
Otolemur garnettii	ENSOGAG00000031228	7 retrocopies	retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps	ENSOPRG00000005059	1 retrocopy	retro_opri_433,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015199	3 retrocopies	retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tupaia belangeri	ENSTBEG00000006212	1 retrocopy	retro_tbel_3864,
Tursiops truncatus	ENSTTRG00000009500	1 retrocopy	retro_ttru_1524,