RetrogeneDB ID: retro_ptro_1241

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 17:72026665..72026986(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSPTRG00000007525
• Aliases: None
• Description: DNA-directed RNA polymerase subunit [Source:UniProtKB/TrEMBL;Acc:H2QA65]

Sequence

>retro_ptro_1241
ATGCTGCTGTTCTACCCTGGCTGCAGGGACGGGCTGATCGTGGAGGAGGGACAGCGCTGCCACCGCCTCGCCTGCAACAC
GTGCCTCTGTGTGCACTTCACCCACAAGGTAACAAATTGGAAGTACTCAAAGCTGAAAGAAGTGGATGATGGGCTTGGGG
GAGCAGCTGCCTGGGAGGATGTTGACTCTACTGCAGAGCCATGTCCTCAATGAGAACCTCCTTGTGCTTACTACATGTAG
CTTCAGACCCACTCTGCAGATGAGCCAAAGACCACCTTCTACCAGTGCTGCAGGGCTCAGTGTGGACACCACTGGAGGGA
T

Alignment

ORF - retro_ptro_1241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTNRKYPKLKEVDDVLGGAAAWENVDSTAEPCP
          MLLF.PGC..GLIVEEGQRCHR.ACNTC..VH..T.KVTN.KY.KLKEVDD.LGGAAAWE.VDSTAEPCP
Retrocopy MLLFYPGCRDGLIVEEGQRCHRLACNTCLCVH-FTHKVTNWKYSKLKEVDDGLGGAAAWEDVDSTAEPCP

Parental  KCEHPRAYFMQLQTRSADEPMTTFYKCCNAQCGHRWRD
          ..E.P.AY.M.LQT.SADEP.TTFY.CC.AQCGH.WRD
Retrocopy Q*EPPCAYYM*LQTHSADEPKTTFYQCCRAQCGHHWRD

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	12.74 RPM
SRP007412_cerebellum	0.11 RPM	12.80 RPM
SRP007412_heart	0.00 RPM	4.90 RPM
SRP007412_kidney	0.00 RPM	11.74 RPM
SRP007412_liver	0.00 RPM	9.39 RPM
SRP007412_testis	0.84 RPM	3.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1241 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1241 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1241 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1861

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978, retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241 ,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,