RetrogeneDB ID: retro_pabe_3558

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:3003506..3003868(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RARRES2
• Ensembl ID: ENSPPYG00000018166
• Aliases: None
• Description: Retinoic acid receptor responder protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R551]

Sequence

>retro_pabe_3558
CACCTGCCCATGCAGTGTGCTTCCAGGAGACCAGTGTGGACAGCACTGTGGACATGCTTGTCCCAGCTGGAGCATTTGTG
AGGCTGGAATTTAAGCTCAGGCAGACAAGCAGCCAGAAGAAGGACTGGAGGAAACCTGAGTGCAAAGTCCATCCCAATGA
GAGGGAGCAGAAATGCTTGGCCTGCATCAAACTTGGCTCTGAGGAGAAAGTTCCGGGCAGGATGAATCACTACCATATAG
AGACACAGGCTTGGCGGGAGCCTGAGGAGCACCAGGGACCCAGTGCAGCAGGGTGGATTGGGCAGTGAGGACCCTGCAGC
TACTGCTTCCTTGCAAAGTTTGCCTTCTTGAAGGCCCAGCCC

Alignment

ORF - retro_pabe_3558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.87 %
• Parental protein coverage: 74.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HPPVQWA-FQETSVESAVDTPFPAGIFVRLEFKLQQTSCRKRDWKKPECKVRPNGRKRKCLACIKLGSED
          H.P.Q.A.FQETSV.S.VD...PAG.FVRLEFKL.QTS..K.DW.KPECKV.PN.R..KCLACIKLGSE.
Retrocopy HLPMQCA<FQETSVDSTVDMLVPAGAFVRLEFKLRQTSSQKKDWRKPECKVHPNEREQKCLACIKLGSEE

Parental  KVLGRLVHCPIETQVLREPEEHQ-ETQCIRVQRA-GEDPH-SFYFPGQFAFSKALP
          KV.GR..H..IETQ..REPEEHQ..TQC.RV..A..EDP..S..F...FAF.KA.P
Retrocopy KVPGRMNHYHIETQAWREPEEHQ<GTQCSRVDWA<SEDPA<SYCFLAKFAFLKAQP

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	16.81 RPM
SRP007412_cerebellum	0.00 RPM	8.03 RPM
SRP007412_heart	0.00 RPM	7.53 RPM
SRP007412_kidney	0.00 RPM	181.38 RPM
SRP007412_liver	0.00 RPM	384.91 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3558 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 79 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010322	5 retrocopies	retro_cjac_2100, retro_cjac_2706, retro_cjac_3874, retro_cjac_3904, retro_cjac_4141,
Homo sapiens	ENSG00000106538	13 retrocopies	retro_hsap_1678, retro_hsap_1679, retro_hsap_1680, retro_hsap_1681, retro_hsap_1682, retro_hsap_1683, retro_hsap_2665, retro_hsap_3134, retro_hsap_4327, retro_hsap_4330, retro_hsap_4332, retro_hsap_4792, retro_hsap_743,
Gorilla gorilla	ENSGGOG00000011158	1 retrocopy	retro_ggor_2984,
Macaca mulatta	ENSMMUG00000005232	4 retrocopies	retro_mmul_1555, retro_mmul_1993, retro_mmul_2378, retro_mmul_2554,
Nomascus leucogenys	ENSNLEG00000001362	18 retrocopies	retro_nleu_1108, retro_nleu_1744, retro_nleu_2079, retro_nleu_2944, retro_nleu_2978, retro_nleu_2999, retro_nleu_3000, retro_nleu_3001, retro_nleu_3034, retro_nleu_3036, retro_nleu_3067, retro_nleu_3071, retro_nleu_3072, retro_nleu_3076, retro_nleu_3089, retro_nleu_3092, retro_nleu_3119, retro_nleu_3128,
Pongo abelii	ENSPPYG00000018166	28 retrocopies	retro_pabe_1382, retro_pabe_1383, retro_pabe_1384, retro_pabe_1386, retro_pabe_1387, retro_pabe_1423, retro_pabe_1424, retro_pabe_1425, retro_pabe_1426, retro_pabe_2404, retro_pabe_2591, retro_pabe_2593, retro_pabe_2595, retro_pabe_2596, retro_pabe_2597, retro_pabe_2600, retro_pabe_2604, retro_pabe_2605, retro_pabe_2606, retro_pabe_2608, retro_pabe_3540, retro_pabe_3558 , retro_pabe_3559, retro_pabe_3604, retro_pabe_3727, retro_pabe_638, retro_pabe_639, retro_pabe_666,
Pan troglodytes	ENSPTRG00000019854	10 retrocopies	retro_ptro_1095, retro_ptro_1096, retro_ptro_1097, retro_ptro_1098, retro_ptro_1099, retro_ptro_1100, retro_ptro_1795, retro_ptro_2942, retro_ptro_3067, retro_ptro_3188,