RetrogeneDB ID: retro_ptro_551

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:71192891..71193201(+)
• Located in intron of: ENSPTRG00000004046

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSPTRG00000002875
• Aliases: None
• Description: None

Sequence

>retro_ptro_551
GCCACCACTGCCACCACCTTGAGTCAGGAGAACCAAGCCCAGGCTGGGGTGTTGGAAGTCTGGGGATTCCAGCCTCAGTC
ACTATGGACAGTTTTTTCTTCATCTGTAGCTCTCTGGCCACACCCACTCCTTTACATTCAAGGTAGAGGAATAAGATAAT
ATGAAGCATGTGCTGGCATTAATTATGCTCTGCTTCACCAAGGGAGCTAACAATGAGTGTAATGTGATAGAAGGTGTAAC
CTGGAACTGTGACCACCAGGAGATTATAGTCCCTCTGGCAAACCTCAAGTTGTCCTGTCAACCCAAGTTA

Alignment

ORF - retro_ptro_551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.98 %
• Parental protein coverage: 58.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAALAFLSQESRTRAG-GVGGLRVPAPVTMDSFFFGCE-LSGHTRSFTFKVEEEDDAEHVLALTMLCLTE
          A.....LSQE....AG.GVG.L..PA.VTMDSFFF.C..LSGHT.SFTFKVEE.D...HVLAL.MLC.T.
Retrocopy ATTATTLSQENQAQAG<GVGSLGIPASVTMDSFFFICS<LSGHTHSFTFKVEE*DNMKHVLALIMLCFTK

Parental  GAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPML
          GA..ECNV.E.V..N.DHQEI.VP.ANLKLSCQP.L
Retrocopy GANNECNVIEGVTWNCDHQEIIVPLANLKLSCQPKL

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	0.04 RPM	16.93 RPM
SRP007412_cerebellum	0.00 RPM	5.74 RPM
SRP007412_heart	0.00 RPM	6.18 RPM
SRP007412_kidney	0.00 RPM	14.51 RPM
SRP007412_liver	0.00 RPM	15.97 RPM
SRP007412_testis	0.00 RPM	11.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_551 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_551 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_792
Pongo abelii	retro_pabe_706
Macaca mulatta	retro_mmul_1072

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551 ,