RetrogeneDB ID: retro_ptro_1179

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:45358135..45358576(+)
• Located in intron of: ENSPTRG00000008776

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSPTRG00000004679
• Aliases: None
• Description: None

Sequence

>retro_ptro_1179
GCCATGAAGAGTGACTTTTATCTGCGCTACTACGTGGGGCACAAGGGCAAGTTCAGCCACGAGTTTCTGGAGTTTGAGTT
CTGACCGGACGGGAAATTAAGATAAGCCAACACAGCAATTACAAGAATGATGTCATGATCAGAAAAGAGGCTTATGTACA
TAAAAGTATGATGGAGGAACTGAAGAGTATAATTGATGACAGTGAAATTACCAAAGAGGATGATGCATTATGGCCTCCTC
CCAACCGAGTGGGCCGGCAGGAGCTTGAAATCATTATTGGAGATGAACACATTTCTTTTACAACATCAAAAATTGGTTCC
CTTATTGATGTCAGTCAATCCAAGGATCCAGAAGGCTTATGAGTATTTTATTATCCTGTCCAGGACCCTGAAGTGTTTGG
TCTTCAGTCTTACTGGATTACACTTCAAGATTAAACCAATC

Alignment

ORF - retro_ptro_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.93 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYAN-NSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
          AM.SDFYLRYYVGHKGKF.HEFLEFEF.PDGKLR.AN..SNYKNDVMIRKEAYVHKS.MEELK.IIDDSE
Retrocopy AMKSDFYLRYYVGHKGKFSHEFLEFEF*PDGKLR*AN<HSNYKNDVMIRKEAYVHKSMMEELKSIIDDSE

Parental  ITKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQD-LKCLVFSLI
          ITKEDDALWPPP.RVGRQELEI.IGDEHISFTTSKIGSLIDV.QSKDPEGL.VFYY.VQD.LKCLVFSL.
Retrocopy ITKEDDALWPPPNRVGRQELEIIIGDEHISFTTSKIGSLIDVSQSKDPEGL*VFYYPVQD>LKCLVFSLT

Parental  GLHFKIKPI
          GLHFKIKPI
Retrocopy GLHFKIKPI

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	0.32 RPM	3.07 RPM
SRP007412_cerebellum	1.04 RPM	4.16 RPM
SRP007412_heart	0.32 RPM	3.09 RPM
SRP007412_kidney	0.84 RPM	4.29 RPM
SRP007412_liver	1.37 RPM	7.01 RPM
SRP007412_testis	1.05 RPM	5.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1179 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1179 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1803
Gorilla gorilla	retro_ggor_1326
Pongo abelii	retro_pabe_1479
Macaca mulatta	retro_mmul_1246

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Callithrix jacchus	ENSCJAG00000021662	7 retrocopies	retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250, retro_cjac_546,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens	ENSG00000111196	1 retrocopy	retro_hsap_1360,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Nomascus leucogenys	ENSNLEG00000003355	1 retrocopy	retro_nleu_1395,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Pan troglodytes	ENSPTRG00000000753	1 retrocopy	retro_ptro_2156,
Pan troglodytes	ENSPTRG00000004679	2 retrocopies	retro_ptro_1179 , retro_ptro_932,
Ictidomys tridecemlineatus	ENSSTOG00000000835	1 retrocopy	retro_itri_212,
Tupaia belangeri	ENSTBEG00000014820	7 retrocopies	retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta	ENSTSYG00000010452	7 retrocopies	retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,