RetrogeneDB ID: retro_mmus_539

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:27280724..27281199(+)
• Located in intron of: ENSMUSG00000019899

Retrocopy information

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

Parental gene information

• Parental gene symbol: Npm1
• Ensembl ID: ENSMUSG00000057113
• Aliases: Npm1, B23, NO38, Npm
• Description: nucleophosmin 1 [Source:MGI Symbol;Acc:MGI:106184]

Sequence

>retro_mmus_539
GACTTGCTGGACATGGTATAAACCCTTTTAGGCTTCAGAACTACCTTTTCAGTTGTGAACTAAAGGCTGACAAAGATTAT
CACTTTAAAGTGGATAATGATGAAGATGAGCATCAGCTATCATTAAGAATGGTCAGTTGAGGGTCAGGGGCAAAAGATGA
ATTACACATTATAGATACAGAAGCAATGAACCATAAAGACAGTCCAATTAAAGTAAAACTAGCAACTCTGAAAAAGTCTG
TACAACCCACAGCTTCCCATGGGGGCTTTGTGGTCATACCAGCTGTAGTATTAAGGTTGAAGTGTGGTTCAGGGTCTGTG
CACATTTGTGGACAGCACCTCGAAGCTGTAGAGGAAGACATAGAGTCAGTAGATGAATACGAGGATGAGGATGATGTAAA
AGTCTTAAGTATGTCTGGAAATTGATCTACTCCTGGAGATAACAAGGTTCTACAGAAAAAGTAAAACTTGATAAA

Alignment

ORF - retro_mmus_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 55.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSMDM-DMSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSP
          D..DM....P.R.QNYLF.CELKADKDYHFKVDNDE.EHQLSLR.VS.G.GAKDELHI...EAMN...SP
Retrocopy DLLDM<GINPFRLQNYLFSCELKADKDYHFKVDNDEDEHQLSLRMVS*GSGAKDELHIIDTEAMNHKDSP

Parental  IKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAESED--EDEEDVKLLGMS
          IKV.LATLK.SVQPT.S.GGF...P.VVLRLKCGSG.VHI.GQHL.AVEED.ES.D..EDE.DVK.L.MS
Retrocopy IKVKLATLKKSVQPTASHGGFVVIPAVVLRLKCGSGSVHICGQHLEAVEEDIESVDEYEDEDDVKVLSMS

Parental  GKRSAPGGGNKVPQK-KVKLDE
          G..S.P.G.NKV.QK.KVKLD.
Retrocopy GN*STP-GDNKVLQK<KVKLDK

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	0.02 RPM	73.57 RPM
SRP007412_cerebellum	0.00 RPM	80.20 RPM
SRP007412_heart	0.00 RPM	66.87 RPM
SRP007412_kidney	0.00 RPM	103.18 RPM
SRP007412_liver	0.00 RPM	81.95 RPM
SRP007412_testis	0.00 RPM	144.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_539 was not detected

EST

No EST(s) were mapped for retro_mmus_539 retrocopy.

TSS

No TSS is located nearby retro_mmus_539 retrocopy 5' end.

Lab

retro_mmus_539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_539 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003910	1 retrocopy	retro_amel_983,
Bos taurus	ENSBTAG00000015316	2 retrocopies	retro_btau_538, retro_btau_56,
Canis familiaris	ENSCAFG00000016912	3 retrocopies	retro_cfam_22, retro_cfam_286, retro_cfam_900,
Callithrix jacchus	ENSCJAG00000019334	13 retrocopies	retro_cjac_1559, retro_cjac_1682, retro_cjac_1696, retro_cjac_1733, retro_cjac_2075, retro_cjac_2351, retro_cjac_2368, retro_cjac_2533, retro_cjac_2605, retro_cjac_3270, retro_cjac_3416, retro_cjac_4117, retro_cjac_838,
Equus caballus	ENSECAG00000021950	4 retrocopies	retro_ecab_1016, retro_ecab_1100, retro_ecab_393, retro_ecab_544,
Felis catus	ENSFCAG00000030268	3 retrocopies	retro_fcat_156, retro_fcat_376, retro_fcat_720,
Homo sapiens	ENSG00000181163	30 retrocopies	retro_hsap_1275, retro_hsap_129, retro_hsap_1526, retro_hsap_1580, retro_hsap_1593, retro_hsap_1621, retro_hsap_2226, retro_hsap_2375, retro_hsap_2478, retro_hsap_2856, retro_hsap_2862, retro_hsap_3355, retro_hsap_3460, retro_hsap_3609, retro_hsap_3636, retro_hsap_3718, retro_hsap_3776, retro_hsap_3808, retro_hsap_3817, retro_hsap_3822, retro_hsap_3962, retro_hsap_4666, retro_hsap_4753, retro_hsap_4785, retro_hsap_614, retro_hsap_638, retro_hsap_690, retro_hsap_717, retro_hsap_785, retro_hsap_961,
Gorilla gorilla	ENSGGOG00000007220	12 retrocopies	retro_ggor_1543, retro_ggor_1660, retro_ggor_1976, retro_ggor_2453, retro_ggor_2454, retro_ggor_2539, retro_ggor_2559, retro_ggor_2571, retro_ggor_2681, retro_ggor_2959, retro_ggor_560, retro_ggor_591,
Macaca mulatta	ENSMMUG00000015781	1 retrocopy	retro_mmul_203,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Mus musculus	ENSMUSG00000057113	5 retrocopies	retro_mmus_1301, retro_mmus_1798, retro_mmus_3131, retro_mmus_539 , retro_mmus_550,
Oryctolagus cuniculus	ENSOCUG00000011117	1 retrocopy	retro_ocun_412,
Otolemur garnettii	ENSOGAG00000013616	14 retrocopies	retro_ogar_1554, retro_ogar_1623, retro_ogar_1671, retro_ogar_1776, retro_ogar_2015, retro_ogar_2168, retro_ogar_2207, retro_ogar_2461, retro_ogar_2605, retro_ogar_2832, retro_ogar_3037, retro_ogar_536, retro_ogar_595, retro_ogar_614,
Pongo abelii	ENSPPYG00000016037	7 retrocopies	retro_pabe_2405, retro_pabe_3072, retro_pabe_3261, retro_pabe_3627, retro_pabe_3699, retro_pabe_486, retro_pabe_532,
Pteropus vampyrus	ENSPVAG00000002211	1 retrocopy	retro_pvam_851,