RetrogeneDB ID: retro_pabe_1479

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:10845676..10846114(-)
• Located in intron of: ENSPPYG00000007986

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOH
• Ensembl ID: ENSPPYG00000001335
• Aliases: None
• Description: mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]

Sequence

>retro_pabe_1479
ATGGAGAGTGACTTTTATCTATGCTACTACGTGGGGCACAAGGGCAAGTTCAGCCATGAGTTTCTGGAGTTTGAGTTCTG
ACCAGACGGGAAATTAAGATAAGCCAACACAGCAATTACAAGAATGATGTCATGATTAGAAAAGAGGCTTATGTACATAA
AAGCATGATGGAGGAACTGAAGAGTGTAATTTATGACAGTGAAATTACCAAACAGGATGATGCGTTATGGCTTCCTCCCA
ACCGAGTGGGCCGGCAGGAGCTTGAAATCATTATTGGAGATGAACACATTTCTTTTACAACATCAAAAACTGGTTCCCTC
ATTGATGTCAATCAATCCAAGGATCCAGAAGGCTTACAAGTATTTTATTATCCTGTCCAGGACCCTGAAGTGTTTGATCT
TCAGTCTTATTGGATTACACTTCAAGATTAAACCAATC

Alignment

ORF - retro_pabe_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MESDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYAN-NSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEI
          MESDFYL.YYVGHKGKF.HEFLEFEF.PDGKLR.AN..SNYKNDVMIRKEAYVHKS.MEELK..I.DSEI
Retrocopy MESDFYLCYYVGHKGKFSHEFLEFEF*PDGKLR*AN<HSNYKNDVMIRKEAYVHKSMMEELKSVIYDSEI

Parental  TKEDDALWPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQD-LKCLVFSLIG
          TK.DDALW.PP.RVGRQELEI.IGDEHISFTTSK.GSLIDVNQSKDPEGL.VFYY.VQD.LKCL.FSLIG
Retrocopy TKQDDALWLPPNRVGRQELEIIIGDEHISFTTSKTGSLIDVNQSKDPEGLQVFYYPVQD>LKCLIFSLIG

Parental  LHFKIKPI
          LHFKIKPI
Retrocopy LHFKIKPI

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	0.28 RPM	10.73 RPM
SRP007412_cerebellum	1.58 RPM	13.86 RPM
SRP007412_heart	0.15 RPM	8.37 RPM
SRP007412_kidney	0.36 RPM	17.14 RPM
SRP007412_liver	1.47 RPM	12.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1479 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1479 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1479 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1803
Pan troglodytes	retro_ptro_1179
Gorilla gorilla	retro_ggor_1326
Macaca mulatta	retro_mmul_1246

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004538	1 retrocopy	retro_cjac_1902,
Cavia porcellus	ENSCPOG00000011511	1 retrocopy	retro_cpor_338,
Homo sapiens	ENSG00000162385	2 retrocopies	retro_hsap_1803, retro_hsap_3318,
Gorilla gorilla	ENSGGOG00000007594	2 retrocopies	retro_ggor_1303, retro_ggor_1326,
Microcebus murinus	ENSMICG00000006406	2 retrocopies	retro_mmur_70, retro_mmur_781,
Myotis lucifugus	ENSMLUG00000002444	1 retrocopy	retro_mluc_1844,
Nomascus leucogenys	ENSNLEG00000017987	2 retrocopies	retro_nleu_2515, retro_nleu_2682,
Oryctolagus cuniculus	ENSOCUG00000001880	5 retrocopies	retro_ocun_1295, retro_ocun_1720, retro_ocun_1872, retro_ocun_1915, retro_ocun_1923,
Otolemur garnettii	ENSOGAG00000013328	2 retrocopies	retro_ogar_1954, retro_ogar_24,
Ochotona princeps	ENSOPRG00000009020	1 retrocopy	retro_opri_521,
Pongo abelii	ENSPPYG00000001335	2 retrocopies	retro_pabe_1479 , retro_pabe_2733,
Pan troglodytes	ENSPTRG00000000753	1 retrocopy	retro_ptro_2156,
Rattus norvegicus	ENSRNOG00000012778	1 retrocopy	retro_rnor_1168,
Ictidomys tridecemlineatus	ENSSTOG00000001253	3 retrocopies	retro_itri_373, retro_itri_379, retro_itri_932,
Tupaia belangeri	ENSTBEG00000011611	17 retrocopies	retro_tbel_1016, retro_tbel_1120, retro_tbel_1213, retro_tbel_140, retro_tbel_1513, retro_tbel_185, retro_tbel_2030, retro_tbel_2031, retro_tbel_2349, retro_tbel_2355, retro_tbel_2525, retro_tbel_3186, retro_tbel_328, retro_tbel_4512, retro_tbel_4540, retro_tbel_735, retro_tbel_809,