RetrogeneDB ID: retro_mmus_1229

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:108672313..108672548(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H2afv
• Ensembl ID: ENSMUSG00000041126
• Aliases: H2afv, C530002L11Rik, H2a.z-2, H2av
• Description: H2A histone family, member V [Source:MGI Symbol;Acc:MGI:1924855]

Sequence

>retro_mmus_1229
GTGGATGTAACAAACATTTGTTTTGGTACAGACATTATTTCCACTCTGGTTATAAAGTTACTTGCTTTGTCTGGGAATGC
ATCAAAAGATGTAAAGGTAAATTGTATTTCCACTGGTCACTTGCAACCTGCTATTCATGGAGATAAAGAATTGGACTATC
TGATCAAGGCTAATTGCTGGTGGTGGTGTCATTCCTCACACCATAAATCTGATTGGGAAGAAGGGACAGGAGGAG

Alignment

ORF - retro_mmus_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.85 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKAT-IAGGGVIPHIH
          V..T.......I...L....L.L.GNASKD.KV..I...HLQ.AI.GD.ELD.LIKA....GG.VIPH..
Retrocopy VDVTNICFGTDIISTLVIKLLALSGNASKDVKVNCISTGHLQPAIHGDKELDYLIKAN>AGGG-VIPHT-

Parental  KSLIGKKGQQK
          ..LIGKKGQ..
Retrocopy INLIGKKGQEE

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	20.79 RPM
SRP007412_cerebellum	0.00 RPM	25.88 RPM
SRP007412_heart	0.00 RPM	38.48 RPM
SRP007412_kidney	0.00 RPM	35.25 RPM
SRP007412_liver	0.00 RPM	23.95 RPM
SRP007412_testis	0.00 RPM	17.24 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1229 was not detected

EST

No EST(s) were mapped for retro_mmus_1229 retrocopy.

TSS

No TSS is located nearby retro_mmus_1229 retrocopy 5' end.

Lab

retro_mmus_1229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1229 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016975	1 retrocopy	retro_btau_686,
Choloepus hoffmanni	ENSCHOG00000000889	3 retrocopies	retro_chof_1967, retro_chof_2205, retro_chof_576,
Callithrix jacchus	ENSCJAG00000011953	1 retrocopy	retro_cjac_3029,
Cavia porcellus	ENSCPOG00000000769	1 retrocopy	retro_cpor_37,
Dipodomys ordii	ENSDORG00000000793	5 retrocopies	retro_dord_100, retro_dord_12, retro_dord_171, retro_dord_195, retro_dord_291,
Erinaceus europaeus	ENSEEUG00000015817	2 retrocopies	retro_eeur_359, retro_eeur_476,
Felis catus	ENSFCAG00000010271	2 retrocopies	retro_fcat_373, retro_fcat_617,
Homo sapiens	ENSG00000105968	2 retrocopies	retro_hsap_1612, retro_hsap_890,
Myotis lucifugus	ENSMLUG00000014500	2 retrocopies	retro_mluc_1492, retro_mluc_2122,
Mus musculus	ENSMUSG00000037894	6 retrocopies	retro_mmus_2397, retro_mmus_2780, retro_mmus_2976, retro_mmus_3039, retro_mmus_3585, retro_mmus_953,
Mus musculus	ENSMUSG00000041126	2 retrocopies	retro_mmus_1229 , retro_mmus_1481,
Ornithorhynchus anatinus	ENSOANG00000009378	2 retrocopies	retro_oana_55, retro_oana_87,
Oryctolagus cuniculus	ENSOCUG00000008133	10 retrocopies	retro_ocun_1226, retro_ocun_1336, retro_ocun_1456, retro_ocun_1596, retro_ocun_1938, retro_ocun_385, retro_ocun_389, retro_ocun_523, retro_ocun_601, retro_ocun_778,
Otolemur garnettii	ENSOGAG00000025145	1 retrocopy	retro_ogar_3181,
Ochotona princeps	ENSOPRG00000015604	3 retrocopies	retro_opri_315, retro_opri_538, retro_opri_942,
Pelodiscus sinensis	ENSPSIG00000005931	1 retrocopy	retro_psin_62,
Pan troglodytes	ENSPTRG00000019153	1 retrocopy	retro_ptro_1081,
Pteropus vampyrus	ENSPVAG00000001109	3 retrocopies	retro_pvam_1284, retro_pvam_165, retro_pvam_213,
Rattus norvegicus	ENSRNOG00000007026	5 retrocopies	retro_rnor_1410, retro_rnor_1815, retro_rnor_1935, retro_rnor_2102, retro_rnor_2310,
Sus scrofa	ENSSSCG00000016738	1 retrocopy	retro_sscr_152,
Ictidomys tridecemlineatus	ENSSTOG00000011533	1 retrocopy	retro_itri_148,
Tupaia belangeri	ENSTBEG00000013840	5 retrocopies	retro_tbel_1155, retro_tbel_1295, retro_tbel_2747, retro_tbel_3214, retro_tbel_970,
Vicugna pacos	ENSVPAG00000004507	1 retrocopy	retro_vpac_608,