RetrogeneDB ID: retro_ptro_1587

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2A:32290292..32290989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AK2
• Ensembl ID: ENSPTRG00000000499
• Aliases: None
• Description: None

Sequence

>retro_ptro_1587
ATGGCTCCCAGCGTGCCAGCGGCAGAACCCGAGTATCCTAAAGGCATCCAGGCCGTGCTGCTGGGGCCTCCTGGGGACGG
TAAAGGCACCCAGGCACCCATATTGGCTGAAAACTTCTGTGTCTGCCATTCGGCTACTGGGGACAGGCTGAGGGCCATGG
TGGCTTCTGGCTCAGAGCTAGAAAAAAAGCTGAAGGCAACTATGGATGCTGGGAAACTGGTGAGTGATGAAATGGTAGTG
GAGCTTATTGAGAAGAATTTGGAGACCCCCCTTGTGCAAAAATGTTTTTCTTCTGGATGGCTTCCCTCGGACTGTGAGGC
AGGCAGAAATGCTCGATGACCTCATGGAGAAGAGGAAAAAGAAGCTTGATTCTGTGATTGAATTCAGCATCCCAGACTCT
CTGCTGATCCGAAGAATCACAGGAAGGCTGATTCACCCCAAGAGTGGCCGTTCCTACTATGAGGAGTTCAACCCTCCAAA
AGAGCTCATGAAAGATGACATCACCGGGGAACCCTTGATTCGTCGATCAGATGATAATGAAAACGCCTTGAAAATCCGCC
TGCAAGCCTACGACACTCCAACCACCCCACTCATAGAGTACTTCAGGAAACGGGAGATCCACTCTGCCATTGATGCATCC
CAGACCCCTGATGTCGTGTTCGCAAGCACCCTAGCAGCCTTCTCCAAAGCCACATCC

Alignment

ORF - retro_ptro_1587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSVPAAEPEYPKGIRAVLLGPPGAGKGTQAPRLAENFCVCHLATGDMLRAMVASGSELGKKLKATMDA
          MAPSVPAAEPEYPKGI.AVLLGPPG.GKGTQAP.LAENFCVCH.ATGD.LRAMVASGSEL.KKLKATMDA
Retrocopy MAPSVPAAEPEYPKGIQAVLLGPPGDGKGTQAPILAENFCVCHSATGDRLRAMVASGSELEKKLKATMDA

Parental  GKLVSDEMVVELIEKNLETPL-CKNGFLLDGFPRTVRQAEMLDDLMEKRKEKLDSVIEFSIPDSLLIRRI
          GKLVSDEMVVELIEKNLETPL.CKN.FLLDGFPRTVRQAEMLDDLMEKRK.KLDSVIEFSIPDSLLIRRI
Retrocopy GKLVSDEMVVELIEKNLETPL>CKNVFLLDGFPRTVRQAEMLDDLMEKRKKKLDSVIEFSIPDSLLIRRI

Parental  TGRLIHPKSGRSYHEEFNPPKEPMKDDITGEPLIRRSDDNEKALKIRLQAYHTQTTPLIEYYRKRGIHSA
          TGRLIHPKSGRSY.EEFNPPKE.MKDDITGEPLIRRSDDNE.ALKIRLQAY.T.TTPLIEY.RKR.IHSA
Retrocopy TGRLIHPKSGRSYYEEFNPPKELMKDDITGEPLIRRSDDNENALKIRLQAYDTPTTPLIEYFRKREIHSA

Parental  IDASQTPDVVFASILAAFSKATS
          IDASQTPDVVFAS.LAAFSKATS
Retrocopy IDASQTPDVVFASTLAAFSKATS

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	0.05 RPM	29.03 RPM
SRP007412_cerebellum	0.14 RPM	49.54 RPM
SRP007412_heart	0.00 RPM	48.50 RPM
SRP007412_kidney	0.13 RPM	116.95 RPM
SRP007412_liver	0.23 RPM	133.03 RPM
SRP007412_testis	0.63 RPM	38.68 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1587 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1587 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1965

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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,