RetrogeneDB ID: retro_pabe_348

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:208381455..208381790(+)
• Located in intron of: ENSPPYG00000001755

Retrocopy information

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

Parental gene information

• Parental gene symbol: MPHOSPH6
• Ensembl ID: ENSPPYG00000007592
• Aliases: None
• Description: M-phase phosphoprotein 6 [Source:HGNC Symbol;Acc:7214]

Sequence

>retro_pabe_348
ATGGCACCTGAGCACAAGACCAAGTTCTCCAAGAACCTGCTGCACATGAAGTTCATGCAAAGAGGACTGGACTCAGAAAC
TAAGAAATGACTAGAAGAGGAAGAAAATAAAATTAGTTAAGAGCAGTGGTACTCAGATTTGCCAGAACTTAATAAAAGTA
AAGAATTTCATAACAGAAGAGCAGCATCTCTTGTTGTGTGAAGATCATTTCTATGGAAGGAATTTCATTCATCAGATTTA
CTCCTGAGGTTGAGAAATTAATGCTTCAGATGAATACTAAGAACAAAGCAGAAATTGAAGATGAAACAGTGGAATTTTAC
GTGTCAGATGAAGAA

Alignment

ORF - retro_pabe_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.17 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAERKTKLSKNLLRMKFMQRGLDSETKKQLEEEEKKIISEEHWYLDLPELKEK-ESFIIEEQSFLLCED
          MA.E.KTK.SKNLL.MKFMQRGLDSETKK.LEEEE.K.IS.E.WY.DLPEL......FI.EEQ..LLCED
Retrocopy MAPEHKTKFSKNLLHMKFMQRGLDSETKK*LEEEENK-IS*EQWYSDLPELNKS>KNFITEEQHLLLCED

Parental  LLYGR-MSFRGFNPEVEKLMLQMNAKHKAEEVEDETVELDVSDEE
          ..YGR..SF..F.PEVEKLMLQMN.K.KA.E.EDETVE..VSDEE
Retrocopy HFYGR>ISFIRFTPEVEKLMLQMNTKNKA-EIEDETVEFYVSDEE

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_prefrontal_cortex	0.00 RPM	10.95 RPM
SRP007412_cerebellum	0.12 RPM	13.62 RPM
SRP007412_heart	0.09 RPM	4.52 RPM
SRP007412_kidney	0.07 RPM	7.03 RPM
SRP007412_liver	0.03 RPM	6.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_348 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_348 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_348 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_353
Pan troglodytes	retro_ptro_277
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,