RetrogeneDB ID: retro_pabe_3148

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:63903069..63903416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSPPYG00000017619
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_pabe_3148
TTCCATTGTGTTTTCTCTATTACAGAAATGGAATCCTTTGCAGCTACAGTTGACTTCAAGGAGCAGATTTAAGAGTAAAA
GAAGATGAGAATATTCCATTTCTACTGGTTGGTAACAAGTCAGATTTAGAAGATAAAAGGCAGGTTTCTATAGAAGAGGC
AAAAAACAGAGCTGACTAGTGGAATGTTAACTATGTGGAAACATCTGCTAAAACACGAGCTAATGTTGACAAAGTATTTT
TTGACTTAATGAGAGAAATTCGAGTGAGAAAGATGGAAGATGACAAAGAGTGGAAAAAGAAGAGGAAAAGTTTAACCGAG
ACAATCAGAGAAAGATCCTGCATTTTA

Alignment

ORF - retro_pabe_3148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 57.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLCVFSITEMESFAATADFREQI-LRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETS
          F.CVFSITEMESFAAT.DF.EQI.LRVKEDEN.PFLLVGNKSDLEDKRQVS.EEAKNRA..WNVNYVETS
Retrocopy FHCVFSITEMESFAATVDFKEQI<LRVKEDENIPFLLVGNKSDLEDKRQVSIEEAKNRAD*WNVNYVETS

Parental  AKTRANVDKVFFDLMREIRARKMEDSKEKNGKKKRKSLAKRIRERCCIL
          AKTRANVDKVFFDLMREIR.RKMED.KE...KKKRKSL...IRER.CIL
Retrocopy AKTRANVDKVFFDLMREIRVRKMEDDKE--WKKKRKSLTETIRERSCIL

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	15.20 RPM
SRP007412_cerebellum	0.00 RPM	12.16 RPM
SRP007412_heart	0.00 RPM	9.30 RPM
SRP007412_kidney	0.00 RPM	12.60 RPM
SRP007412_liver	0.00 RPM	11.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3148 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3148 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3148 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3707
Pan troglodytes	retro_ptro_2511
Macaca mulatta	retro_mmul_1706

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
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	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,