RetrogeneDB ID: retro_ptro_2511

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:19203401..19203748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSPTRG00000019108
• Aliases: None
• Description: None

Sequence

>retro_ptro_2511
TTCCACTGTGTCTTCTCTATTACAGAAATGGAATCCTTTGCAGCTACAGTTGACTTCAAGGAGCAGATTTAAGAGTAAAA
GAAGAAGAGAATATTCCATTTCTACTGGTTGGTAACAAATCAGATTTAGAAGATAAAAGGCAGGTTTCTATAGAAGAGGC
AAAAAACAGAGCTGACTAGTGGAATGTTATCTGTGTGGAAACATCTCCTAAAACATGAGCTAATGTTCACAAGGTATTTT
TTGACTTAATGAGAGAAATTCGAGTGAGAAAGATGGAAGGTGACAAAGAGTGGAAAAAGAAGAGGAAAAGTTTAGCCAAG
ACAATCAGAGAAAGATGCTGCATTTTA

Alignment

ORF - retro_ptro_2511 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 57.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLCVFSITEMESFAATADFREQI-LRVKEDENVPFLLVGNKSDLEDKRQVSVEEAKNRAEQWNVNYVETS
          F.CVFSITEMESFAAT.DF.EQI.LRVKE.EN.PFLLVGNKSDLEDKRQVS.EEAKNRA..WNV..VETS
Retrocopy FHCVFSITEMESFAATVDFKEQI<LRVKEEENIPFLLVGNKSDLEDKRQVSIEEAKNRAD*WNVICVETS

Parental  AKTRANVDKVFFDLMREIRARKMEDSKEKNGKKKRKSLAKRIRERCCIL
          .KT.ANV.KVFFDLMREIR.RKME..KE...KKKRKSLAK.IRERCCIL
Retrocopy PKT*ANVHKVFFDLMREIRVRKMEGDKE--WKKKRKSLAKTIRERCCIL

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	33.01 RPM
SRP007412_cerebellum	0.00 RPM	25.56 RPM
SRP007412_heart	0.00 RPM	18.86 RPM
SRP007412_kidney	0.00 RPM	27.01 RPM
SRP007412_liver	0.00 RPM	23.57 RPM
SRP007412_testis	0.00 RPM	24.87 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2511 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2511 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2511 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3707
Pongo abelii	retro_pabe_3148
Macaca mulatta	retro_mmul_1706

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 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	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Pan troglodytes	ENSPTRG00000005197	3 retrocopies	retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
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,