RetrogeneDB ID: retro_ptro_855

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:22363717..22364478(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSPTRG00000002516
• Aliases: None
• Description: None

Sequence

>retro_ptro_855
AGAAGATTCAGCAAGTACCCATTAATGGAAGAGATTGGGTTTCTTGGTGCTTGGCATGAGGGTTTACCATGTTCATTCCG
ATAGCTATGATATACAAAACCAGCATTATGGAAGAAGCTTAACAAAAGGAACTATAAAGGATGGAGTCTCTGGATTTTTT
CATAATGGGTACTGCTTAAGAAAAGATGCTGTTGCTGCCAGTATTCAGAAGATTGAGAAAATTCTGCAGTGGTTTGAAAA
CCAGAAGCAGCTTAACTTTTATGCAAGTTCATTACTATTGGTTTATGAAAGTTCATCTCAGCCAACCACTACAAAATTGA
ATGACAGAACTTTGGCAGAAAAGTTTTTGTCCAAAGGACAACTGTCAGACACAGAGGTACTAGAGTACAATAATAACTTT
CATGTATTAAGTTCCACAGTGAATGGAAAAATAGAGGCTTAAGTGGGCAAAAACTTGTCCAAGATGTATGCTCGTCACAG
GAAAATGTATACAAAAACCATCACAGTCAGACTTCAATGAAAGTTGAAAATCTGGAGCAAGACAATGGGTGGAAAAGCAT
GTCACAGAACATTTAAATGGAAATGTACTTTCCCAACTGGAAAAAGTTTTCTACCATCTTCCCACTGGTTGCCAAGAGAT
TGCTGAAGTAGGAGTGCGAATGATAGATTTTGCTCATGTGTTCCCTAGCAGCACAATAGATGAGGGATATATTTATGGGC
TAAAGCATTTAATTTCTGTACTTCGAAGTATTTTAGACAAT

Alignment

ORF - retro_ptro_855 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.05 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQVSKYPLMEEIGFL-VLGMRVYHVHSDSYETQNQHYGRSLTKETIKDGVSRFFHNGYCLRKDAVAASIQ
          ...SKYPLMEEIGFL.VLGMRVYHVHSDSY..QNQHYGRSLTK.TIKDGVS.FFHNGYCLRKDAVAASIQ
Retrocopy RRFSKYPLMEEIGFL>VLGMRVYHVHSDSYDIQNQHYGRSLTKGTIKDGVSGFFHNGYCLRKDAVAASIQ

Parental  KIEKILQWFENQKQLNFYASSLLFVYEGSSQPTTTKLNDRTLAEKFLSKGQLSDTEVLEYNNNFHVLSST
          KIEKILQWFENQKQLNFYASSLL.VYE.SSQPTTTKLNDRTLAEKFLSKGQLSDTEVLEYNNNFHVLSST
Retrocopy KIEKILQWFENQKQLNFYASSLLLVYESSSQPTTTKLNDRTLAEKFLSKGQLSDTEVLEYNNNFHVLSST

Parental  ANGKIESSVGKSLSKIYARHRKIYT-KKHHSQTSLKVENLEQDNGWKSMSQ-EHLNGNVLSQLEKVFYHL
          .NGKIE..VGK.LSK.YARHRK.YT.K.HHSQTS.KVENLEQDNGWKSMSQ.EHLNGNVLSQLEKVFYHL
Retrocopy VNGKIEA*VGKNLSKMYARHRKMYT<KNHHSQTSMKVENLEQDNGWKSMSQ<EHLNGNVLSQLEKVFYHL

Parental  PTGCQEIAEVEVRMIDFAHVFPSNTIDEGYVYGLKHLISVLRSILDN
          PTGCQEIAEV.VRMIDFAHVFPS.TIDEGY.YGLKHLISVLRSILDN
Retrocopy PTGCQEIAEVGVRMIDFAHVFPSSTIDEGYIYGLKHLISVLRSILDN

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	5.70 RPM
SRP007412_cerebellum	0.00 RPM	5.81 RPM
SRP007412_heart	0.00 RPM	2.86 RPM
SRP007412_kidney	0.03 RPM	5.73 RPM
SRP007412_liver	0.00 RPM	4.06 RPM
SRP007412_testis	0.21 RPM	5.27 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_855 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_855 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_855 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1244

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855 ,