RetrogeneDB ID: retro_pabe_1672

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:33952817..33953765(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP468E1617
• Ensembl ID: ENSPPYG00000018017
• Aliases: None
• Description: None

Sequence

>retro_pabe_1672
ATGGCCAGCCACCTTGTGCTCAACAGTGGTACCAAGATGCCCATCCTGGGGCTGGGCACCTGGAAGTCCCCTCCAGGCTG
CGTGACTGAGGCCGTGAAGGTGGCCATCAATGTCAGGTACTGCCACATTGACTGTGCCCACGTGTACTAGAATGAGAATG
AGGTGGGGGTAGCCATTCAGGAGAAGCTCAGGGAGCAGGCGGTGAAGCGTGAGGAGCTCTTCATCGTTAGTAAACTGTGG
TGCACATACCATGGGAAGGGCCTGGTGAAAGGAGCTTGCCAGAAGACCCTCAGCAGCCTGAAGCTGGACTACCTGGACCT
CTACCTTATTCACTGGCCAACTGGCTTTAAGCCTGGGAAGGAATTTTTCCATTGAATGAGTTGGGTAATGTGGTTCCCAG
TGACACCAACATTCTGGACACATGGGCAGCCATGGAAGAGCTGGTGGATGAACAGCTGGTGAAAGCTATTGGCATCTCCA
ACTTCAACCATCTCCAGGTGGAGAGGCTCTTAAACAAACCTGGCTTAAAGTATAAGCCTGTGGTTAACTAGATGGAGTGC
CACCCTTACCTCACTCAGGAGAAGTTAATCCAGTACTGCCAGTCCAAAGGCATCGTGGTGACCGCCTGTAGCCCCCTCGG
CACTCCCATCAGGCCCTGGGCCAACCCCGAGGACCCTTCCCTCCTGGGGGATCCCAGGACCAAGGCGATTGCAGCCAAGC
ACAGTAAAACTACAGCCCAGGTCCTGATCCGGTTCCCCATGCAGAGGAACTTGGGGGTGATTCCCCAAGTCTGTGACACC
AGAACTCATTGCTGACAACTTTAAGGTTTTTGACTTTGAACTGAACAGCCAGGATATGACCGCCTTACTCAGCTACAACA
GGAACTGGAGGGTCTGTGCCTTGATGAGCTGTGCCTCCCACAAGGATTACCCCTTCCATGAAGAGTTT

Alignment

ORF - retro_pabe_1672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASHLVLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKR
          MASHLVLN.G.KMPILGLGTWKSPPG.VTEAVKVAI.V.Y.HIDCAHVY.NENEVGVAIQEKLREQ.VKR
Retrocopy MASHLVLNSGTKMPILGLGTWKSPPGCVTEAVKVAINVRYCHIDCAHVY*NENEVGVAIQEKLREQAVKR

Parental  EELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFF-PLDESGSVVPSDTNIL
          EELFIVSKLWCTYH.KGLVKGACQKTLS.LKLDYLDLYLIHWPTGFKPGKEFF.PL.E.G.VVPSDTNIL
Retrocopy EELFIVSKLWCTYHGKGLVKGACQKTLSSLKLDYLDLYLIHWPTGFKPGKEFF<PLNELGNVVPSDTNIL

Parental  DTWAAMEELVDEGLVKAIGISNFNHLQVETILNKPGLKYNPAVNQIECHPYLTQEKLIQYCQSKGIVVTA
          DTWAAMEELVDE.LVKAIGISNFNHLQVE..LNKPGLKY.P.VN..ECHPYLTQEKLIQYCQSKGIVVTA
Retrocopy DTWAAMEELVDEQLVKAIGISNFNHLQVERLLNKPGLKYKPVVN*MECHPYLTQEKLIQYCQSKGIVVTA

Parental  YSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVI-PKSVTPERIAENFKVFD
          .SPLG.P.RPWA.PEDPSLL.DPR.KAIAAKH.KTTAQVLIRFPMQRNL.VI.PKSVTPE.IA.NFKVFD
Retrocopy CSPLGTPIRPWANPEDPSLLGDPRTKAIAAKHSKTTAQVLIRFPMQRNLGVI>PKSVTPELIADNFKVFD

Parental  FELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
          FEL.SQDMT.LLSYNRNWRVCAL.SC.SHKDYPFHEEF
Retrocopy FELNSQDMTALLSYNRNWRVCALMSCASHKDYPFHEEF

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	60.99 RPM
SRP007412_cerebellum	0.00 RPM	66.88 RPM
SRP007412_heart	0.00 RPM	14.45 RPM
SRP007412_kidney	0.00 RPM	20.05 RPM
SRP007412_liver	0.00 RPM	8.94 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1672 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1672 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1672 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009902	3 retrocopies	retro_btau_1092, retro_btau_1642, retro_btau_821,
Canis familiaris	ENSCAFG00000001290	1 retrocopy	retro_cfam_63,
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973, retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Dasypus novemcinctus	ENSDNOG00000011358	2 retrocopies	retro_dnov_2214, retro_dnov_721,
Homo sapiens	ENSG00000085662	7 retrocopies	retro_hsap_1261, retro_hsap_1422, retro_hsap_2049, retro_hsap_2663, retro_hsap_312, retro_hsap_4745, retro_hsap_851,
Gorilla gorilla	ENSGGOG00000011731	6 retrocopies	retro_ggor_1477, retro_ggor_1859, retro_ggor_2948, retro_ggor_343, retro_ggor_695, retro_ggor_991,
Macropus eugenii	ENSMEUG00000003434	6 retrocopies	retro_meug_1455, retro_meug_1505, retro_meug_1811, retro_meug_1980, retro_meug_486, retro_meug_504,
Microcebus murinus	ENSMICG00000001921	2 retrocopies	retro_mmur_1087, retro_mmur_66,
Mus musculus	ENSMUSG00000001642	10 retrocopies	retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Nomascus leucogenys	ENSNLEG00000013037	7 retrocopies	retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Otolemur garnettii	ENSOGAG00000016156	2 retrocopies	retro_ogar_1282, retro_ogar_808,
Procavia capensis	ENSPCAG00000016195	1 retrocopy	retro_pcap_428,
Pongo abelii	ENSPPYG00000018017	8 retrocopies	retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672 , retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pongo abelii	ENSPPYG00000018037	1 retrocopy	retro_pabe_406,
Pan troglodytes	ENSPTRG00000019716	6 retrocopies	retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Rattus norvegicus	ENSRNOG00000009513	1 retrocopy	retro_rnor_1438,
Tupaia belangeri	ENSTBEG00000013327	1 retrocopy	retro_tbel_3093,