RetrogeneDB ID: retro_ptro_295

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:47040978..47041464(-)
• Located in intron of: ENSPTRG00000000701

Retrocopy information

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

Parental gene information

• Parental gene symbol: NENF
• Ensembl ID: ENSPTRG00000001961
• Aliases: None
• Description: None

Sequence

>retro_ptro_295
CAGCTGTAGCCACTAGCAGGGTTGACCCTGGTCCTGGTACAGCCCCCAGGGCTGCTTGCAGCTCTGGCCAGGCAGGTGCC
GTGCCTGACTAAGCAGAAACCCCTGGTGAGGCTCTTTATTGAGGAGGAGCCGGCCCACTACGGAGAGAAGAAAAACATCC
CATCTACATGACAGTGAAGGGAGTGGTGTCTTATGTCACCTCCAGAAAGGAATTTTATGGAAGAAGGGGCCCCCTATAAT
GCATTGACCAGGGAAGTCCACCAGAGGGATAGCCAAGATGTCCCTGGGTCCTCCAGACCTCACCCATGAAACTCTGGGTC
TCATGGCCAAAGAGCTGGAATCCCTGGATGATATCTTCACCAAAGTGTACAAAACCAAATATCCCATGGTTAGCTACACA
GTCTGAAGAATTCTTAATAGGGACAGCACCCCAGCCTGGACTTCAAACCTGAAGACCAACCCCATTTTGACATAAACAAT
GTGTTC

Alignment

ORF - retro_ptro_295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 95.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RLRPLAALALVLALAPGLPTARAGQTPRPAERGPPVRLFTEEELARYGGE-EEDQPIYLAVKGVVFDVTS
          .L.PLA.L.LVL...PGL..A.A.Q.P......P.VRLF.EEE.A.Y.GE.EE..PIY..VKGVV..VTS
Retrocopy QL*PLAGLTLVLVQPPGLLAALARQVPCLTKQKPLVRLFIEEEPAHY-GE<EEKHPIYMTVKGVVSYVTS

Parental  GKEFYGR-GAPYNALT-GKDSTRGVAKMSLDPADLTHDTTGLTAKELEALDEVFTKVYKAKYPIVGYTAR
          .KEFYGR.GAPYNALT.GK.STRG.AKMSL.P.DLTH.T.GL.AKELE.LD..FTKVYK.KYP.V.YT..
Retrocopy RKEFYGR>GAPYNALT>GK-STRGIAKMSLGPPDLTHETLGLMAKELESLDDIFTKVYKTKYPMVSYTV*

Parental  RILNEDGS-PNLDFKPEDQPHFDIKDEF
          RILN.D...P.LDFKPEDQPHFDI...F
Retrocopy RILNRDST<PSLDFKPEDQPHFDINNVF

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	0.00 RPM	45.08 RPM
SRP007412_cerebellum	0.00 RPM	25.13 RPM
SRP007412_heart	0.00 RPM	28.21 RPM
SRP007412_kidney	0.03 RPM	59.50 RPM
SRP007412_liver	0.00 RPM	26.97 RPM
SRP007412_testis	0.00 RPM	3.48 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_295 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_295 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_295 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_379
Pongo abelii	retro_pabe_328
Macaca mulatta	retro_mmul_490
Bos taurus	retro_btau_1238

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295 ,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,