RetrogeneDB ID: retro_ptro_656

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:6596177..6596518(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSPTRG00000006911
• Aliases: None
• Description: None

Sequence

>retro_ptro_656
TTGGAGAGCAAGCAATTCCTGACGGAGCTGACCAGACTCTTCCAGAAGTGCCGGACGTTGGGCAGCGTCTATATCACCTT
GAAGAAGTATGATGGTCGAACCAAACCCATTCCAAAGAAAGGTTCTGTGGAGGGCTTTGAGCCCTCAGACAACAAGTGTC
TGTTAAGAGCTATCGATGGGAAAAAGAAGATGAGCACTGTGGTGAACTCCAAGGAAGTGAGTAAGTTTCAGATGGCTTAT
TCAAACCTACTGAGAGCTAACATGGACGGACTGAGAAGAGGGACAAAAAGAGCAAAAGGAAAAAGACCAAAGCAGCAGCA
CAGTAAAGGGCACAAATTCCC

Alignment

ORF - retro_ptro_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 83.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LESEQFLTELTRLFQKCRTSGSVYITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKISTVVSS
          LES.QFLTELTRLFQKCRT.GSVYITLKKYDGRTKPIPKKG.VEGFEP.DNKCLLRA.DGKKK.STVV.S
Retrocopy LESKQFLTELTRLFQKCRTLGSVYITLKKYDGRTKPIPKKGSVEGFEPSDNKCLLRAIDGKKKMSTVVNS

Parental  KEVNKFQMAYSNLLRANMDGLK-KRDKKNKTKKTKAAAAAAAAAP
          KEV.KFQMAYSNLLRANMDGL..KRDKK.K.KKTKAAA...A..P
Retrocopy KEVSKFQMAYSNLLRANMDGLR<KRDKKSKRKKTKAAAQ*RAQIP

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	0.02 RPM	96.43 RPM
SRP007412_cerebellum	0.04 RPM	85.61 RPM
SRP007412_heart	0.00 RPM	92.19 RPM
SRP007412_kidney	0.00 RPM	174.62 RPM
SRP007412_liver	0.03 RPM	85.21 RPM
SRP007412_testis	0.00 RPM	52.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_656 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_656 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_656 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_949
Pongo abelii	retro_pabe_811
Macaca mulatta	retro_mmul_780

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Choloepus hoffmanni	ENSCHOG00000005321	2 retrocopies	retro_chof_212, retro_chof_2659,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Cavia porcellus	ENSCPOG00000008994	2 retrocopies	retro_cpor_1071, retro_cpor_462,
Dasypus novemcinctus	ENSDNOG00000011147	3 retrocopies	retro_dnov_1303, retro_dnov_2164, retro_dnov_2599,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Homo sapiens	ENSG00000140319	3 retrocopies	retro_hsap_1765, retro_hsap_811, retro_hsap_949,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Myotis lucifugus	ENSMLUG00000010531	5 retrocopies	retro_mluc_1489, retro_mluc_2284, retro_mluc_2545, retro_mluc_375, retro_mluc_384,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Nomascus leucogenys	ENSNLEG00000002457	2 retrocopies	retro_nleu_246, retro_nleu_2831,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pan troglodytes	ENSPTRG00000006911	3 retrocopies	retro_ptro_1181, retro_ptro_564, retro_ptro_656 ,
Tupaia belangeri	ENSTBEG00000016637	1 retrocopy	retro_tbel_196,
Tarsius syrichta	ENSTSYG00000009467	4 retrocopies	retro_tsyr_1283, retro_tsyr_1985, retro_tsyr_60, retro_tsyr_73,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,