RetrogeneDB ID: retro_mmus_2972

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:126176123..126176531(+)
• Located in intron of: ENSMUSG00000000131

Retrocopy information

• Ensembl ID: ENSMUSG00000057945
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H3f3b
• Ensembl ID: ENSMUSG00000016559
• Aliases: H3f3b, 9430068D06Rik, H3.3B
• Description: H3 histone, family 3B [Source:MGI Symbol;Acc:MGI:1101768]

Sequence

>retro_mmus_2972
ATTGCTCGTACAAAGCAGACTGCCCGAAAATCCACCGGTGGTAAAGAACCCAGGAAACAACTGGCTACAAAAGCCGCTCG
CAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTTATCGTTACAGGCCTGGTACTGTGGCACTCCGAGAAATCAGAC
GCTATCAGAAGTCCACTGAACTTCTGATCTGCAAGCTCCCCTTTCAGAGTCTGGTTTGAGAAATTGCTCAGGACTTCAAA
ACAGATCTGCGCTTCCTGAGGGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
TATCAACCTGTGTGCTAACCATGCCAAATGTGTAAAAATTATGCCAAAAGATATCCAGCTAGCATGCCACATATGCAGAG
AAAGTGCT

Alignment

ORF - retro_mmus_2972 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
          .ARTKQTARKSTGGK.PRKQLATKAARKSAPSTGGVKKP.RYRPGTVALREIRRYQKSTELLI.KLPFQ.
Retrocopy IARTKQTARKSTGGKEPRKQLATKAARKSAPSTGGVKKPYRYRPGTVALREIRRYQKSTELLICKLPFQS

Parental  LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LV.EIAQDFKTDLRF..AAIGALQEASEAYLVGLFED.NLCA.HAK.V.IMPKDIQLA..I..E.A
Retrocopy LV*EIAQDFKTDLRFLRAAIGALQEASEAYLVGLFEDINLCANHAKCVKIMPKDIQLACHICRESA

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	61.33 RPM
SRP007412_cerebellum	0.00 RPM	106.82 RPM
SRP007412_heart	0.00 RPM	53.36 RPM
SRP007412_kidney	0.00 RPM	84.72 RPM
SRP007412_liver	0.03 RPM	69.99 RPM
SRP007412_testis	0.05 RPM	201.07 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2972 was not detected

EST

No EST(s) were mapped for retro_mmus_2972 retrocopy.

TSS

No TSS is located nearby retro_mmus_2972 retrocopy 5' end.

Lab

retro_mmus_2972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2972 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 134 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Dipodomys ordii	ENSDORG00000008132	9 retrocopies	retro_dord_238, retro_dord_283, retro_dord_43, retro_dord_589, retro_dord_678, retro_dord_685, retro_dord_719, retro_dord_765, retro_dord_774,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Gorilla gorilla	ENSGGOG00000022526	11 retrocopies	retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Mus musculus	ENSMUSG00000016559	18 retrocopies	retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972 , retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Pongo abelii	ENSPPYG00000000168	14 retrocopies	retro_pabe_1285, retro_pabe_2151, retro_pabe_2204, retro_pabe_2252, retro_pabe_2391, retro_pabe_2679, retro_pabe_2722, retro_pabe_2805, retro_pabe_2938, retro_pabe_3078, retro_pabe_323, retro_pabe_3420, retro_pabe_3637, retro_pabe_3697,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Rattus norvegicus	ENSRNOG00000003220	4 retrocopies	retro_rnor_121, retro_rnor_191, retro_rnor_336, retro_rnor_44,