RetrogeneDB ID: retro_pabe_1132

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:75674232..75674520(+)
• Located in intron of: ENSPPYG00000005987

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSPPYG00000001028
• Aliases: None
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_pabe_1132
CAGTCCACGTTTGACTTACAGGACCTGAGGGAACAGATTTTACTGGTTAAGGACACAGAAGATGTTCCAATGATTTTGGT
TGGCAATAAATGTGACCTGGAAGATGAGTGAGTAGTCGGCAAAGAACAGGGCCAGAATTTAGCATGACAGTGATGGAACT
GTGCCATTTTAGAATAATCTGCAAAGTCAAAGGTCAATGTTAACGAAATATTTTATGACCTGGTCAGACAGATAAATAGA
AAAACACCAGTGGAAAAGAAACAGCCTAAAAAGAAATCATGCCTGCTG

Alignment

ORF - retro_pabe_1132 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 52.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNE
          QSTF.DLQDLREQIL.VKDTEDVPMILVGNKCDLEDE.VVGKEQGQNLA.Q..NCA.LE.SAKSK.NVNE
Retrocopy QSTF-DLQDLREQILLVKDTEDVPMILVGNKCDLEDE*VVGKEQGQNLA*Q*WNCAILE*SAKSKVNVNE

Parental  IFYDLVRQINRKTPVEKKKPKKKSCLL
          IFYDLVRQINRKTPVEKK.PKKKSCLL
Retrocopy IFYDLVRQINRKTPVEKKQPKKKSCLL

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	21.90 RPM
SRP007412_cerebellum	0.00 RPM	20.92 RPM
SRP007412_heart	0.03 RPM	19.27 RPM
SRP007412_kidney	0.07 RPM	29.93 RPM
SRP007412_liver	0.00 RPM	20.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1132 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1132 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1132 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1364
Pan troglodytes	retro_ptro_937
Callithrix jacchus	retro_cjac_728

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132 ,
Pongo abelii	ENSPPYG00000004369	1 retrocopy	retro_pabe_2870,
Pongo abelii	ENSPPYG00000004751	1 retrocopy	retro_pabe_3403,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,