RetrogeneDB ID: retro_ptro_284

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:29972234..29972724(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA20
• Ensembl ID: ENSPTRG00000013299
• Aliases: NAA20, NAT5
• Description: None

Sequence

>retro_ptro_284
ACACTCAGGACCCCCATCTGTGATGACCTGTCCCACTTAGACAACACCAACATGGGTCCACTTACAGAAACTTTGTACTT
ACAGAACCTCACCCACTGGCCAGAGTATTTGATAGCTACAGAGGTGCTTGGAGAGCTTATGGATCACATGATGGGTAAAA
TAAATGTTTCTCTCGTAGCTAGGGAAGAATTTCACAGGCATGTCACAGCCTTCTCTGTTGTCCTGGAATTTCCATGCCTT
GGTTTGGCCGCTGAACTAATGGAGGAGAATTCCAAAAGAAAGGGTGATTTTGAAATGGATCTCTCAATAAGAGCATCCAA
TCATGTTTCAGTCAACATGTACATACAGTTGGGCAAACTTCATGTACAAGATCATCTTACCATCATCAAGTACTCAACTT
GCAAATGAAGATGCTTGTGATAAGAGGAAAGCATTTTCACAGAAATCTGTGATACCATTACCTCATTCCGGGAGGCCTGA
AGATACTGAA

Alignment

ORF - retro_ptro_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.37 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TLRAFTCDDLFRFNNINLDPLTETYGIPFYLQYLAHWPEYFIVAEAPGGELMGYIMGKAEGS-VAREEWH
          TLR...CDDL....N.N..PLTET.....YLQ.L.HWPEY.I..E...GELM...MGK...S.VAREE.H
Retrocopy TLRTPICDDLSHLDNTNMGPLTET----LYLQNLTHWPEYLIATEVL-GELMDHMMGKINVSLVAREEFH

Parental  GHVTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLG-YSVYRTVIEYYSA
          .HVTA.SV..EF..LGLAA.LME...E.S.RKG.F..DL..R.SN.V.VNMY.QLG....Y.......S.
Retrocopy RHVTAFSVVLEFPCLGLAAELME---ENSKRKGDFEMDLSIRASNHVSVNMYIQLG>NFMYKIILPSSST

Parental  SNGEPDEDAYDMRKALSRDTEKKSIIPLPHPVRPEDIE
          .....D..A.D.RKA.S.....KS.IPLPH..RPED.E
Retrocopy QLANED--ACDKRKAFS----QKSVIPLPHSGRPEDTE

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	26.22 RPM
SRP007412_cerebellum	0.00 RPM	27.42 RPM
SRP007412_heart	0.03 RPM	26.44 RPM
SRP007412_kidney	0.00 RPM	41.11 RPM
SRP007412_liver	0.00 RPM	34.53 RPM
SRP007412_testis	0.00 RPM	181.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_284 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_284 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_374
Pongo abelii	retro_pabe_342

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001144	1 retrocopy	retro_btau_899,
Canis familiaris	ENSCAFG00000032025	1 retrocopy	retro_cfam_768,
Callithrix jacchus	ENSCJAG00000005377	4 retrocopies	retro_cjac_1099, retro_cjac_1629, retro_cjac_2984, retro_cjac_439,
Gorilla gorilla	ENSGGOG00000004247	1 retrocopy	retro_ggor_374,
Microcebus murinus	ENSMICG00000006044	1 retrocopy	retro_mmur_540,
Macaca mulatta	ENSMMUG00000007708	1 retrocopy	retro_mmul_479,
Mustela putorius furo	ENSMPUG00000001228	2 retrocopies	retro_mputfur_1495, retro_mputfur_321,
Mus musculus	ENSMUSG00000002728	3 retrocopies	retro_mmus_1228, retro_mmus_3146, retro_mmus_3257,
Nomascus leucogenys	ENSNLEG00000009855	1 retrocopy	retro_nleu_2267,
Oryctolagus cuniculus	ENSOCUG00000015481	1 retrocopy	retro_ocun_1331,
Otolemur garnettii	ENSOGAG00000011542	1 retrocopy	retro_ogar_2007,
Pongo abelii	ENSPPYG00000010746	1 retrocopy	retro_pabe_342,
Pan troglodytes	ENSPTRG00000013299	1 retrocopy	retro_ptro_284 ,
Ictidomys tridecemlineatus	ENSSTOG00000014733	1 retrocopy	retro_itri_1656,
Tupaia belangeri	ENSTBEG00000000969	1 retrocopy	retro_tbel_567,