RetrogeneDB ID: retro_pabe_3628

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:36340056..36341070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSPPYG00000001483
• Aliases: None
• Description: Nuclear transcription factor Y subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q5RA23]

Sequence

>retro_pabe_3628
GAGGCATTTTTCAAAACATCCACAGAATGTGGATTTTGTGGCATTAGCAGCAGTAGTGCCCAGTAAAGCCTACAGTCCTT
TTGGGCTTCACATCCTGGAAGAAATCCAGAATTTAACAGTGAAAGATTTACTAGTGCAGGAACTTCCATGGCTGGTATTA
AGAAGATTATGAAACTGAATGATGTAAAGATGATCAGCGGAGAAGCTCCTGTGCTCTTTGCCAAGGCAGCCCGGACTTTT
ATCACAGAGTTGACTCTTTGAGCCTAGATTCACACAGAGGCTAAAAAGCACTGGACTCTATAGGGAAATGATGTCACCAT
GGGAATTACAAAATTAGATCAGTTAGACTTTCTCATTGATATTGTTTTCACAGATGAACTGAACCCTCCAAAGCATCAGG
AGGAGGTGTGCCAGTCTATAACTCCTGCCAAGCCCATCTAGTACTACCTCATGCTGGCTTAGCAGCCCTCCACTGTCCAA
GTCTAGGGACAGCAGCAAGGCCAGGAGACCACCAGCTCTATGACCACCATCCAACTTGGGTAGATCATCATGCAGCCTCA
GCAGGGCCAGATCATGCCCCTGACAATGCAGGTTGGAGAAGGTCGACAGGTGCAGATTGTCCAGGCCCAACCACAGGGTC
AAGCCTAACAGTCCTAGAGTGACACTGGACAGACTATGCAGGTTATGCAACAGATTATTACTAAAACAGGAGAGATCCAG
CAGATCCCAGTGCAGCTGAAGTTGGGCCAGCTAGAATATATTCTCTTAGTCCAGGCTGTATCAGGTACTCAAGTCGTGCA
GGAACAGACTTAGATGCTTGCCACCAATGCCCAACAGATTACATAGACAGAGGTCCAGTAAGGACAGCGGCAGTTCAACC
AGGTCACAGATGGACACAAGCTCTACCAGATCCAGTAAGTCACCATTCCTGTGGACTAGGACCTCACCCAGCCCATGTTC
AACCAGTCAGCCAACCAGCTCTCCTACAGGCAGGACCCCCAGGTGACCCACGAC

Alignment

ORF - retro_pabe_3628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 95.77 %
• Number of stop codons detected: 15
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEVVEMSTEGGFGGTSSSDAQQSLQSFWP-RVMEEIRNLTVKDFRVQELP-LARIKKIMKLDEDVKMISA
          E.....STE.GF.G.SSS.AQ.SLQSFW.....EEI.NLTVKD..VQELP..A.IKKIMKL..DVKMIS.
Retrocopy EAFFKTSTECGFCGISSSSAQ*SLQSFWA>HILEEIQNLTVKDLLVQELP<MAGIKKIMKLN-DVKMISG

Parental  EAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEDVR
          EAPVLFAKAA..FITELTL.A.IHTE..K..TL..ND..M.ITK.DQ.DFLIDIV..DEL.PPK.QE.V.
Retrocopy EAPVLFAKAARTFITELTL*A*IHTEAKKHWTL*GNDVTMGITKLDQLDFLIDIVFTDELNPPKHQEEVC

Parental  QSVTPAEPVQYYFTLAQQPAAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQI
          QS.TPA.P..YY..LA.QP..VQV.GQQQGQ.TTSS.TTIQ.G.II..QPQQGQ..P.TMQVGEG.QVQI
Retrocopy QSITPAKPI*YYLMLA*QPSTVQV*GQQQGQETTSSMTTIQLG*IIM-QPQQGQIMPLTMQVGEGRQVQI

Parental  VQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATN
          VQAQPQGQA.Q..S.TGQTMQVMQQIIT.TGEIQQIPVQL..GQL.YI.L.Q.VSGTQVVQ.Q...LATN
Retrocopy VQAQPQGQA*QS*SDTGQTMQVMQQIITKTGEIQQIPVQLKLGQLEYILLVQAVSGTQVVQEQT*MLATN

Parental  AQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAPQVTGD
          AQQIT.TEVQ.GQ.QF.Q.TDG..LYQIQ.VT.P...DL.QPMF.QSANQ.S..Q.PQVT.D
Retrocopy AQQIT*TEVQ*GQRQFNQVTDGHKLYQIQ*VTIPVD*DLTQPMFNQSANQLSYRQDPQVTHD

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	30.74 RPM
SRP007412_cerebellum	0.00 RPM	31.25 RPM
SRP007412_heart	0.00 RPM	13.67 RPM
SRP007412_kidney	0.00 RPM	29.20 RPM
SRP007412_liver	0.00 RPM	22.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3628 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3628 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4668
Pan troglodytes	retro_ptro_3102
Gorilla gorilla	retro_ggor_2896

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 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,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369, retro_nleu_2850,
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 ,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,