RetrogeneDB ID: retro_ptro_3102

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:36104831..36105653(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSPTRG00000000596
• Aliases: None
• Description: None

Sequence

>retro_ptro_3102
ATGTCCACAGAATGTGGATTTTGTGGCACTAGCAGCAGTAATGCCCAGTAAAGCCTACAGTCCTTTTGGGCTTCACATCC
TGGAAGAAATCCAGAATTTAACAGTGAAAGATTTACTAGTGCAGGAACTTCCACAGCTGGTATTAAGAAGATTATGAAAC
TGAATGATGTAAAGATGATCAGTAGAGGAGCTCCTGTGCTCTTTGCCAAGGCAGCCCAGATTTTTATCACAGAGTTGACT
CTTTGAGCCTAGATTCACACAGAGGCTAAAAAGCACTGGACTCTATAGGGAAATGATGTCACCATGGGAATTACAAAATT
AGATCAGTTAGACTTTCTCATTGATATTGTTTTGACAGATGAACTGAACCCTCCAAAGTGTCAGGAGGAGGTGTGCCAGT
CTATAACTCCTGCTAAGCCCATCTAGTACTACTTCACACTGGCTTAGCAGCCCTCCACGGTCCAAGTCTAGGGACAGCAG
CAAGGCCAGGAGACCACCAGCTCTATGACCACCATCCAGCTTGGGTAGATCATCATGCAGCCTCAGCAGGGCCAAATCAT
GCCCCCGACAGTGCAGGTTGGAGAAGGTCGGCAGGTGCAGATTGTCCAGGCCCAACCGCAGGGTCAAGCCTAACAGTCCT
AGAGTGACACTGGACAGACTATGGAAGTTATGCAACAGATTATTACTAAAACAGGAGAGATCCAGCAGATCCCAGTGCAA
CTGAAGTTGGGCCAGCTAGAATATATTCTCTTAGTCCAGCCTGTATCAGGTACTCAAGTCGTGCAGGAACAGATATAGAT
GCTTGCCACCAATGCCCAACAG

Alignment

ORF - retro_ptro_3102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.82 %
• Parental protein coverage: 77.97 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGTSSSDAQQSLQSFWP-RVMEEIRNLTVKDFRVQELP-LARIKKIMKLDEDVKMISAEAPVL
          MSTE.GF.GTSSS.AQ.SLQSFW.....EEI.NLTVKD..VQELP..A.IKKIMKL..DVKMIS..APVL
Retrocopy MSTECGFCGTSSSNAQ*SLQSFWA>HILEEIQNLTVKDLLVQELP<TAGIKKIMKLN-DVKMISRGAPVL

Parental  FAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTP
          FAKAAQIFITELTL.A.IHTE..K..TL..ND..M.ITK.DQ.DFLIDIV..DEL.PPK.QEEV.QS.TP
Retrocopy FAKAAQIFITELTL*A*IHTEAKKHWTL*GNDVTMGITKLDQLDFLIDIVLTDELNPPKCQEEVCQSITP

Parental  AEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQP
          A.P..YYFTLA.QP..VQV.GQQQGQ.TTSS.TTIQ.G.II..QPQQGQ..P.T.QVGEG.QVQIVQAQP
Retrocopy AKPI*YYFTLA*QPSTVQV*GQQQGQETTSSMTTIQLG*IIM-QPQQGQIMPPTVQVGEGRQVQIVQAQP

Parental  QGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQ
          QGQA.Q..S.TGQTM.VMQQIIT.TGEIQQIPVQL..GQL.YI.L.QPVSGTQVVQ.QI..LATNAQQ
Retrocopy QGQA*QS*SDTGQTMEVMQQIITKTGEIQQIPVQLKLGQLEYILLVQPVSGTQVVQEQI*MLATNAQQ

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	47.39 RPM
SRP007412_cerebellum	0.00 RPM	53.34 RPM
SRP007412_heart	0.00 RPM	28.50 RPM
SRP007412_kidney	0.00 RPM	51.36 RPM
SRP007412_liver	0.00 RPM	32.64 RPM
SRP007412_testis	0.00 RPM	36.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3102 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3102 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4668
Gorilla gorilla	retro_ggor_2896
Pongo abelii	retro_pabe_3628

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102 ,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,