RetrogeneDB ID: retro_ptro_564

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:91328948..91329286(+)
• Located in intron of: ENSPTRG00000004174

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_564
ATGGTGTTGTTAGAGAGCGAGCAGCTCCTGACGGAGCTGACCAGACTTTTCCAGAAGTGCTGGACATCAGGCAGCATCAT
ATCACCTTGAAGAAGTATGACAGTCGAACCAAATCCATTCCAAAGAAAGGTACTGTGGAGGGCTTTGAGCCTGCAGACAA
CAAGTGTCTGTTAAGAGCTACCGATGGGAAAAAGAAGATCAGCACAGTGGTGAGCTCCAAGGAAGTGAGTAAGTTTCAGA
TGGCTTATTCAAACCTCCTGAGAGCTAACATGGATGGGCTGAAGAAGAGAGACAAAAAGAACAAAACTAAGAAGACCAAA
GCAGCAGCAACAGCAGCA

Alignment

ORF - retro_ptro_564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 83.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRTSGSV-YITLKKYDGRTKPIPKKGTVEGFEPADNKCLLRATDGKKKIST
          MVLLESEQ.LTELTRLFQKC.TSGS...ITLKKYD.RTK.IPKKGTVEGFEPADNKCLLRATDGKKKIST
Retrocopy MVLLESEQLLTELTRLFQKCWTSGSI<HITLKKYDSRTKSIPKKGTVEGFEPADNKCLLRATDGKKKIST

Parental  VVSSKEVNKFQMAYSNLLRANMDGLKKRDKKNKTKKTKAAAAAA
          VVSSKEV.KFQMAYSNLLRANMDGLKKRDKKNKTKKTKAAA.AA
Retrocopy VVSSKEVSKFQMAYSNLLRANMDGLKKRDKKNKTKKTKAAATAA

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	0.05 RPM	96.43 RPM
SRP007412_cerebellum	0.07 RPM	85.61 RPM
SRP007412_heart	0.03 RPM	92.19 RPM
SRP007412_kidney	0.03 RPM	174.62 RPM
SRP007412_liver	0.03 RPM	85.21 RPM
SRP007412_testis	0.11 RPM	52.69 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_564 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_564 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_811
Gorilla gorilla	retro_ggor_665

---

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,