RetrogeneDB ID: retro_ptro_33

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:154979905..154980346(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000034202
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSPTRG00000003333
• Aliases: None
• Description: Pan troglodytes ribosomal protein L27a (RPL27A), mRNA. [Source:RefSeq mRNA;Acc:NM_001034084]

Sequence

>retro_ptro_33
ATGCCATCCAGACTGAGGAAGACCCGGAAACTTAGGGGCCACGTGAGCCACGGCCACGGCCGCTTGGGCAAGCACCGGAA
GCACCCCGGCGGCCGCGGTAATGCTGGTGGTCTGCATCACCACCGGATCAACTTCGACAAATACCACCCAGGCTACTTTG
GGAAAGTTGGTATGAAGCATTACCACTTAAAGAGGAACCAGAGCTTCTGCCCAACTGTCAACCTTGACAAATTGTGGACT
TTGGTCAGTGAGCAGACACGGGTGAATGCTGCTAAAAACAAGACTGGGGCTGCTCCCATCATTGATGTGGTGCGATCTGG
CTACTACAAAGTTCTGGGAAAGGGAAAGCTCCCAAAGCAGCCTGTCACCGTGAAGGCCAAATTCTTCAGCAGAAGAGCTA
AGGAGAAGATTAAGAGTGTTGGGGGGGCCTGTGTCCTGGTG

Alignment

ORF - retro_ptro_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.95 %
• Parental protein coverage: 99.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCP
          PSRLRKTRKLRGHVSHGHGR.GKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCP
Retrocopy PSRLRKTRKLRGHVSHGHGRLGKHRKHPGGRGNAGGLHHHRINFDKYHPGYFGKVGMKHYHLKRNQSFCP

Parental  TVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVG
          TVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPV.VKAKFFSRRA.EKIKSVG
Retrocopy TVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQPVTVKAKFFSRRAKEKIKSVG

Parental  GACVLV
          GACVLV
Retrocopy GACVLV

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	0.63 RPM	113.32 RPM
SRP007412_cerebellum	0.25 RPM	102.78 RPM
SRP007412_heart	0.06 RPM	87.90 RPM
SRP007412_kidney	0.21 RPM	187.77 RPM
SRP007412_liver	0.10 RPM	154.18 RPM
SRP007412_testis	0.00 RPM	27.72 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_33 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_33 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3682
Gorilla gorilla	retro_ggor_155

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Homo sapiens	ENSG00000166441	7 retrocopies	retro_hsap_1263, retro_hsap_1908, retro_hsap_2352, retro_hsap_239, retro_hsap_3335, retro_hsap_3586, retro_hsap_3682,
Gorilla gorilla	ENSGGOG00000001660	2 retrocopies	retro_ggor_155, retro_ggor_1785,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Macaca mulatta	ENSMMUG00000021828	2 retrocopies	retro_mmul_207, retro_mmul_268,
Monodelphis domestica	ENSMODG00000007480	1 retrocopy	retro_mdom_575,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Pan troglodytes	ENSPTRG00000003333	1 retrocopy	retro_ptro_33 ,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Tupaia belangeri	ENSTBEG00000000046	20 retrocopies	retro_tbel_1093, retro_tbel_1101, retro_tbel_1148, retro_tbel_1152, retro_tbel_1223, retro_tbel_1338, retro_tbel_1639, retro_tbel_2017, retro_tbel_2606, retro_tbel_2777, retro_tbel_298, retro_tbel_3111, retro_tbel_3496, retro_tbel_3881, retro_tbel_4566, retro_tbel_460, retro_tbel_544, retro_tbel_643, retro_tbel_925, retro_tbel_937,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,
Tarsius syrichta	ENSTSYG00000013207	16 retrocopies	retro_tsyr_1103, retro_tsyr_155, retro_tsyr_1591, retro_tsyr_1607, retro_tsyr_1623, retro_tsyr_170, retro_tsyr_1725, retro_tsyr_187, retro_tsyr_204, retro_tsyr_283, retro_tsyr_498, retro_tsyr_50, retro_tsyr_550, retro_tsyr_608, retro_tsyr_612, retro_tsyr_716,