RetrogeneDB ID: retro_pabe_1965

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:80183275..80183966(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK2
• Ensembl ID: ENSPPYG00000001579
• Aliases: None
• Description: Adenylate kinase 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5REI7]

Sequence

>retro_pabe_1965
ATGGCTCCCAGCGTGCCAGTGGCAGAACCCAAGTACCCTAAAGGCATCCAGGCCGTGCTGCTGGGGCCTCCTGGGGACGG
TAAAGGCACCCAGGCACCCAGATTGGCTGAAAACTTCTGTGTCTGCCATTCGGCTACTGGGGACATGCTGAGGGCCATGG
TGGCTTCTGGCTCAGAGCTAGGAAAAAAGCTGAAGGCAACCATGGATGCTGGGAAACTGGTGAGTGATGAAATGGTAGTG
GAGCTCATTGAGAGGAATTTGGAGACCCCCTTGTGCAAAAATGGTTTTCTTCTGGATGGCTTCCCTCGGACTGTGAGGCA
GGCAGAAATGCTCGATGACCTCATGGAGAAGAGGAAAGAGAAGCTTGATTCTGTGATTGAATTCAGCATCCCAGACTCTG
CTGATCCGAAGAATCACAGGAAGGCTGATTCACCCCAAGAGTGGCGGTTCCTACCACGAGGAGTTCAATCCTCCAAAAGA
GCCCATGAAAGATGACATCACCAGGGTACCCTTGATTCGTCGATCAGATGATAATGAAAAGGGCTTGAAAATCCACCTGC
AAGCCTACCACACTCAAACTACCCCACTCATAGAGTACTACAGGAAACGGGGGATCCACTCTGCCATTGATGCATCCCAG
ACCCCTGATGTCGTGTTCGCAAGCATCCTAGCAGCCTTCTCCAAAGCCACA

Alignment

ORF - retro_pabe_1965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 96.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSVPAAEPEYPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLRAMVASGSELGKKLKATMDA
          MAPSVP.AEP.YPKGI.AVLLGPPG.GKGTQAPRLAENFCVCH.ATGDMLRAMVASGSELGKKLKATMDA
Retrocopy MAPSVPVAEPKYPKGIQAVLLGPPGDGKGTQAPRLAENFCVCHSATGDMLRAMVASGSELGKKLKATMDA

Parental  GKLVSDEMVVELIEKNLETPLCKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIPDS-LLIRRI
          GKLVSDEMVVELIE.NLETPLCKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIPDS.L..R.I
Retrocopy GKLVSDEMVVELIERNLETPLCKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIPDS>LIRR-I

Parental  TGRLIHPKSGRSYHEEFNPPKEPMKDDITGEPLIRRSDDNEKALKIRLQAYHTQTTPLIEYYRKRGIHSA
          TGRLIHPKSG.SYHEEFNPPKEPMKDDIT..PLIRRSDDNEK.LKI.LQAYHTQTTPLIEYYRKRGIHSA
Retrocopy TGRLIHPKSGGSYHEEFNPPKEPMKDDITRVPLIRRSDDNEKGLKIHLQAYHTQTTPLIEYYRKRGIHSA

Parental  IDASQTPDVVFASILAAFSKAT
          IDASQTPDVVFASILAAFSKAT
Retrocopy IDASQTPDVVFASILAAFSKAT

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	0.06 RPM	21.07 RPM
SRP007412_cerebellum	0.12 RPM	71.38 RPM
SRP007412_heart	0.06 RPM	27.54 RPM
SRP007412_kidney	0.60 RPM	149.43 RPM
SRP007412_liver	0.58 RPM	76.35 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1965 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1965 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1587

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017605	2 retrocopies	retro_btau_1146, retro_btau_1168,
Canis familiaris	ENSCAFG00000010390	1 retrocopy	retro_cfam_1622,
Callithrix jacchus	ENSCJAG00000001105	1 retrocopy	retro_cjac_509,
Dasypus novemcinctus	ENSDNOG00000014113	4 retrocopies	retro_dnov_1077, retro_dnov_2052, retro_dnov_2690, retro_dnov_588,
Echinops telfairi	ENSETEG00000002333	2 retrocopies	retro_etel_1466, retro_etel_309,
Homo sapiens	ENSG00000004455	1 retrocopy	retro_hsap_395,
Gorilla gorilla	ENSGGOG00000000069	1 retrocopy	retro_ggor_395,
Myotis lucifugus	ENSMLUG00000000793	1 retrocopy	retro_mluc_1463,
Macaca mulatta	ENSMMUG00000006284	1 retrocopy	retro_mmul_1326,
Monodelphis domestica	ENSMODG00000017363	1 retrocopy	retro_mdom_1792,
Nomascus leucogenys	ENSNLEG00000003152	1 retrocopy	retro_nleu_1313,
Oryctolagus cuniculus	ENSOCUG00000001832	2 retrocopies	retro_ocun_1280, retro_ocun_445,
Otolemur garnettii	ENSOGAG00000000818	1 retrocopy	retro_ogar_2760,
Ochotona princeps	ENSOPRG00000005023	1 retrocopy	retro_opri_822,
Pongo abelii	ENSPPYG00000001579	1 retrocopy	retro_pabe_1965 ,
Pan troglodytes	ENSPTRG00000000499	1 retrocopy	retro_ptro_1587,
Rattus norvegicus	ENSRNOG00000000122	3 retrocopies	retro_rnor_1965, retro_rnor_2315, retro_rnor_974,
Sorex araneus	ENSSARG00000000202	1 retrocopy	retro_sara_556,
Sus scrofa	ENSSSCG00000024355	1 retrocopy	retro_sscr_714,
Ictidomys tridecemlineatus	ENSSTOG00000016042	1 retrocopy	retro_itri_595,
Tursiops truncatus	ENSTTRG00000008979	2 retrocopies	retro_ttru_1579, retro_ttru_978,