RetrogeneDB ID: retro_hsap_353

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:22394993..22395320(-)
• Located in intron of: ENSG00000070831

Retrocopy information

• Ensembl ID: ENSG00000271428
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MPHOSPH6
• Ensembl ID: ENSG00000135698
• Aliases: MPHOSPH6, MPP, MPP-6, MPP6
• Description: M-phase phosphoprotein 6 [Source:HGNC Symbol;Acc:7214]

Sequence

>retro_hsap_353
ATGGCACCTGAGCACAAGACCAAGTTCTCCAAGAACCTGCTGTACATGAAGTTCATGCAAAGAAGACTGGACTCAGAAAC
TAAGAAATGACTAGAAGAGGAAGAAAATAAAATTAGTTAAGAGCACTGGTACTCAGATTTGCCAGAGCTTAATAAGTAAA
GAATTTCATAACAGAAGAGCAGCATCTCTTGTTATGTGAAGATCATTTCTATGGAAGGAATTTCATTCATCAGATTTACT
CCTGAGGTTGAGAAATTAGTGCTTCAGGTGAATACTAAGAACAAAGCAGAAATTGAAGATGAAACAGTGGAATTTTACGT
GTCAGAT

Alignment

ORF - retro_hsap_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.03 %
• Parental protein coverage: 69.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAERKTRLSKNLLRMKFMQRGLDSETKKQLEEEEKKIISEEHWYLDLPELKE-KESFIIEEQSFLLCED
          MA.E.KT..SKNLL.MKFMQR.LDSETKK.LEEEE.K.IS.EHWY.DLPEL......FI.EEQ..LLCED
Retrocopy MAPEHKTKFSKNLLYMKFMQRRLDSETKK*LEEEENK-IS*EHWYSDLPELNK<VKNFITEEQHLLLCED

Parental  LLYGR-MSFRGFNPEVEKLMLQMNAKHKAEEVEDETVELDVSD
          ..YGR..SF..F.PEVEKL.LQ.N.K.KA.E.EDETVE..VSD
Retrocopy HFYGR>ISFIRFTPEVEKLVLQVNTKNKA-EIEDETVEFYVSD

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
bodymap2_adipose	0.10 RPM	12.92 RPM
bodymap2_adrenal	0.59 RPM	14.35 RPM
bodymap2_brain	0.14 RPM	15.12 RPM
bodymap2_breast	0.14 RPM	15.47 RPM
bodymap2_colon	0.00 RPM	15.37 RPM
bodymap2_heart	0.13 RPM	5.06 RPM
bodymap2_kidney	0.04 RPM	16.83 RPM
bodymap2_liver	0.04 RPM	10.29 RPM
bodymap2_lung	0.23 RPM	4.64 RPM
bodymap2_lymph_node	0.33 RPM	7.31 RPM
bodymap2_ovary	0.33 RPM	15.07 RPM
bodymap2_prostate	0.00 RPM	12.96 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.91 RPM
bodymap2_testis	0.21 RPM	22.60 RPM
bodymap2_thyroid	0.09 RPM	11.71 RPM
bodymap2_white_blood_cells	0.00 RPM	10.14 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_353 was not detected

EST

No EST(s) were mapped for retro_hsap_353 retrocopy.

TSS

No TSS is located nearby retro_hsap_353 retrocopy 5' end.

Lab

retro_hsap_353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_353 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_277
Pongo abelii	retro_pabe_348
Macaca mulatta	retro_mmul_471

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000127	2 retrocopies	retro_chof_1602, retro_chof_740,
Callithrix jacchus	ENSCJAG00000016498	5 retrocopies	retro_cjac_1730, retro_cjac_2976, retro_cjac_3135, retro_cjac_3136, retro_cjac_3283,
Dipodomys ordii	ENSDORG00000011060	2 retrocopies	retro_dord_62, retro_dord_63,
Echinops telfairi	ENSETEG00000010276	6 retrocopies	retro_etel_1269, retro_etel_1300, retro_etel_1307, retro_etel_749, retro_etel_795, retro_etel_855,
Homo sapiens	ENSG00000135698	1 retrocopy	retro_hsap_353 ,
Gorilla gorilla	ENSGGOG00000001405	1 retrocopy	retro_ggor_367,
Macropus eugenii	ENSMEUG00000000580	1 retrocopy	retro_meug_726,
Myotis lucifugus	ENSMLUG00000000268	1 retrocopy	retro_mluc_78,
Macaca mulatta	ENSMMUG00000022575	2 retrocopies	retro_mmul_1786, retro_mmul_471,
Mus musculus	ENSMUSG00000031843	2 retrocopies	retro_mmus_1998, retro_mmus_3662,
Nomascus leucogenys	ENSNLEG00000010725	1 retrocopy	retro_nleu_2264,
Oryctolagus cuniculus	ENSOCUG00000024341	2 retrocopies	retro_ocun_1042, retro_ocun_749,
Otolemur garnettii	ENSOGAG00000012532	3 retrocopies	retro_ogar_1288, retro_ogar_1382, retro_ogar_583,
Pongo abelii	ENSPPYG00000007592	1 retrocopy	retro_pabe_348,
Pan troglodytes	ENSPTRG00000008398	1 retrocopy	retro_ptro_277,
Rattus norvegicus	ENSRNOG00000050087	6 retrocopies	retro_rnor_1760, retro_rnor_2298, retro_rnor_2318, retro_rnor_2320, retro_rnor_2390, retro_rnor_2391,
Tupaia belangeri	ENSTBEG00000013110	8 retrocopies	retro_tbel_1037, retro_tbel_1812, retro_tbel_3027, retro_tbel_32, retro_tbel_333, retro_tbel_4213, retro_tbel_4385, retro_tbel_4415,
Tarsius syrichta	ENSTSYG00000001928	2 retrocopies	retro_tsyr_1511, retro_tsyr_906,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.09 RPM
CEU_NA11930	0.03 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.05 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.12 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.03 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.02 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.20 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.08 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.06 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.08 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.04 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).