RetrogeneDB ID: retro_pabe_1086

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:2231064..2231835(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSPPYG00000002433
• Aliases: None
• Description: inositol polyphosphate multikinase [Source:HGNC Symbol;Acc:20739]

Sequence

>retro_pabe_1086
CAACAGGTCAGCAAGTACCCATTAATGGAAGAGATTGGGTTTCTTGGTGCTTGGCATGAGGATTTACCATGTTCATTCCG
ATAGCTATGATATACCAAACCAGCATTATGGAAGAAGCTTAACAAAAGAAACTATAAAGGATGGAGTCTCCGGATTTTTT
CATAATGGGTACTGCTTAAGAAAAGATGCTGTTGCTGCCAGTATTCAGAAGATTGAGAAAATTCTGTAGTGGTGTGAAAA
CCAGAAGCAGCTTAACTTTTATGTCTAAGTTCATTACTATTGGTTTATGAAAGTTCATCTCAGCCAACCACTACAAAATT
GAATGACAGAACTTTGGCAGAAATATTTTTGTCCAAAGGACAACTGTCAGATACAGAGGTACTAGAGTACAATAATAACT
TTCATGTGTTAAGTTCCACAACGAATGGAAAAATAGAGGCTTAAGTGGGCAAAAGCTTGTCCAAGATGTATGCTCGTCAC
AGGAAAAATGTATACAATAAACCATCACAGTCAGACTTCAATGAAAGTTGAAAATCTGCGAGCAAGACAATGGGTGGAAA
AGCATGTCACAGGAACATTTAAATGGAAATGCACTTTCCCAACTGGAAAAAAGGTTTTCTACCATCTTCCCACTGGTTGC
CAAGAGATTGCTGAAGTAGGAGTGCAAAATGATAGATTTTGCTTTATGTGTTCTCTAGCAGCACAATAGATGAGGGATAT
AGTTATGGGCTAAAGCATTTAATTTCTGTACTTCGAAGTATTTTAGACAGT

Alignment

ORF - retro_pabe_1086 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.84 %
• Parental protein coverage: 61.06 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QQVSKYPLMEEIGFL-VLGMRVYHVHSDSYETQNQHYGRSLTKETIKDGVSRFFHNGYCLRKDAVAASIQ
          QQVSKYPLMEEIGFL.VLGMR.YHVHSDSY...NQHYGRSLTKETIKDGVS.FFHNGYCLRKDAVAASIQ
Retrocopy QQVSKYPLMEEIGFL>VLGMRIYHVHSDSYDIPNQHYGRSLTKETIKDGVSGFFHNGYCLRKDAVAASIQ

Parental  KIEKILQWFENQKQLNFY-ASSLLFVYEGSS-QPTTTKLNDRTLAEKFLSKGQLSDTEVLEYNNNFHVLS
          KIEKIL.W.ENQKQLNFY...S.L.....SS.QPTTTKLNDRTLAE.FLSKGQLSDTEVLEYNNNFHVLS
Retrocopy KIEKIL*WCENQKQLNFY<CLSSLLLVYESSSQPTTTKLNDRTLAEIFLSKGQLSDTEVLEYNNNFHVLS

Parental  STANGKIESSVGKSLSKMYARHR-KMYTKKHHSQTSLKVENL-EQDNGWKSMSQEHLNGNVLSQLEKVFY
          ST.NGKIE..VGKSLSKMYARHR.KMYT..HHSQTS.KVENL.EQDNGWKSMSQEHLNGN.LSQLEK.F.
Retrocopy STTNGKIEA*VGKSLSKMYARHR>KMYTINHHSQTSMKVENL>EQDNGWKSMSQEHLNGNALSQLEKRFS

Parental  HL-PTGCQEVAEVEVRMIDFA-HVFPSNTIDEGYVYGLKHLISVLRSILDN
          ...P.........E..MIDFA..VF.S.TIDEGY.YGLKHLISVLRSILD.
Retrocopy TIFPLVAKRLLK*ECKMIDFA>YVFSSSTIDEGYSYGLKHLISVLRSILDS

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	1.11 RPM
SRP007412_cerebellum	0.00 RPM	2.68 RPM
SRP007412_heart	0.00 RPM	0.78 RPM
SRP007412_kidney	0.00 RPM	0.70 RPM
SRP007412_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1086 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1086 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1086 has 0 orthologous retrocopies within eutheria group .

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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,