RetrogeneDB ID: retro_ptro_1781

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:48211476..48211808(+)
• Located in intron of: ENSPTRG00000014873

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000007990
• Aliases: None
• Description: None

Sequence

>retro_ptro_1781
AAGCAGCGTGGCCAGGCCGGGGTCTGAGCTGGGGTTCTGTCCCTGCTGGGCTATGGCCCCAGCTGGACTGCTGCCACAGA
ACTCAGCACCAAATAACTCCAGGAGAAGCTACAGTGGGACCCGGAGGCAAAGCATATGGAGGTGGAGGACGTGACCCTCA
ACCGTCGTGCCTGCAGCTTCCGAGTCCTGGTGGTGTTGGCCAAGTTTGAGGGGAAGCTGCTGCTTCAGACACACTGGCGG
GTAAACATGTGGCTAGCTGGAGGCTCTCGCACATCCATGCTTTTGAGCAGAAAACCCTCATCCCAGAGCAGTGGGCTTGT
GAACGGCAGAAA

Alignment

ORF - retro_ptro_1781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 73.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QQGSVAGVRAGVVSLLGCRFSWTVAMELSAEYLREKLQRNLEAEHVEVEDTTLNRCACSFRVLVVSAKFE
          .Q...AGV.AGV.SLLG...SWT.A.ELS...L.EKLQ...EA.H.EVED.TLNR.ACSFRVLVV.AKFE
Retrocopy KQRGQAGV*AGVLSLLGYGPSWTAATELSTK*LQEKLQWDPEAKHMEVEDVTLNRRACSFRVLVVLAKFE

Parental  GKPLLQRHRLVNACLAE-ELPHIHAFEQKTLTPDQWARERQK
          GK.LLQ.H..VN..LA...L.HIHAFEQKTL.P.QWA.ERQK
Retrocopy GKLLLQTHWRVNMWLAG<RLSHIHAFEQKTLIPEQWACERQK

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	0.18 RPM	14.85 RPM
SRP007412_cerebellum	0.29 RPM	6.38 RPM
SRP007412_heart	0.00 RPM	5.33 RPM
SRP007412_kidney	0.18 RPM	11.82 RPM
SRP007412_liver	0.03 RPM	10.51 RPM
SRP007412_testis	0.21 RPM	12.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1781 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1781 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006661	1 retrocopy	retro_cjac_1327,
Echinops telfairi	ENSETEG00000006548	1 retrocopy	retro_etel_457,
Homo sapiens	ENSG00000169627	1 retrocopy	retro_hsap_2644,
Gorilla gorilla	ENSGGOG00000012724	2 retrocopies	retro_ggor_1847, retro_ggor_75,
Loxodonta africana	ENSLAFG00000017910	1 retrocopy	retro_lafr_712,
Myotis lucifugus	ENSMLUG00000003449	1 retrocopy	retro_mluc_2380,
Macaca mulatta	ENSMMUG00000007331	3 retrocopies	retro_mmul_1344, retro_mmul_1522, retro_mmul_1752,
Monodelphis domestica	ENSMODG00000015658	1 retrocopy	retro_mdom_1704,
Nomascus leucogenys	ENSNLEG00000001018	2 retrocopies	retro_nleu_1222, retro_nleu_650,
Oryctolagus cuniculus	ENSOCUG00000007562	1 retrocopy	retro_ocun_241,
Ochotona princeps	ENSOPRG00000002109	2 retrocopies	retro_opri_243, retro_opri_492,
Pongo abelii	ENSPPYG00000007237	2 retrocopies	retro_pabe_1608, retro_pabe_2326,
Pan troglodytes	ENSPTRG00000007990	2 retrocopies	retro_ptro_1284, retro_ptro_1781 ,
Rattus norvegicus	ENSRNOG00000047988	2 retrocopies	retro_rnor_322, retro_rnor_379,
Sorex araneus	ENSSARG00000003579	2 retrocopies	retro_sara_106, retro_sara_278,
Tarsius syrichta	ENSTSYG00000006274	1 retrocopy	retro_tsyr_1321,
Tursiops truncatus	ENSTTRG00000005543	2 retrocopies	retro_ttru_127, retro_ttru_1700,