RetrogeneDB ID: retro_ggor_2896

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:36388621..36389623(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSGGOG00000007360
• Aliases: None
• Description: None

Sequence

>retro_ggor_2896
AAAATGTCCACAGAATGTGGATTTTGTGGCACTAGCAGCAGTAATGCCCAATAAAGCCTACAGTCCTTTTGGGCTTCACA
TCCTGGAAGAAATCCAGAATTTAACAGTGAAAGATTTACTAGTGCAGGAACTTCCACGGCTGGTATTAAGAAGATTATGA
AACTGAATGATGTAAAGATGATCAGTAGAGAAGCTCCTGTGCTCTTTGCCAAGGCAGCCCAGATTTTTATCACAGAGTTG
ACTCTTTGAGCCTAGATTCACACAGAGGCTAAAAAGCACTGGACTCTATAGGGAAATGATGTCACCATGGTAATTACAAA
ATTAGATCAGTTAGACTTTCTCATTGATATTGTTTTGACAGATGAACTGAACCCTCCAAAGCGTCAGGAGGAGGTGTGCC
AGTCTATAACTCCTGCTAAGCCCATCTAGTACTACTTCACACTGGCTTAGCAGCCCTCCACGGTCCGAGTCTAGGGACAG
CAGCAAGGCCAGGAGACCACCAGCTCTATGACCACCATCCAGCTTGGGTAGATCATCATGCAGCCTCAGCAGGGCCAAAT
CATGCCCCTGACAGTGCAGGTTGGAGAAGGTCGGCAGGTGCAGATTGTCCAGGCCCAACCACAGGGTCAAGCCTAACAGT
CCTAGATTGACACTGGACAGACTATGGAAGTTATGCAACAGATTATTACTAAAACAGGAGAGATCCAGCAGATCCCAGTG
CAGCTGAAGTTGGGCCAGCTAGAATATATTCTCTTAGTCCAGCCTGTATCAGGTACTCAAGTCCTGCAGGAACAGATATA
GATGCTTGCCACCAATGCCCAACAGATTACATAGACAGAGGTCCAGTAAGGACAGCGGCAGTTCAACCAGGTCACAGATG
GACACAAGCTCTACCAGATCCAGCAAGTCACCATTCCTGTGGACTAGGACCTCACCCAGCCCATGTTCAACCAGTCAGTC
AACCAGCTCTCCTACAGGCAGAACCCCCAGGTGACCCATGAC

Alignment

ORF - retro_ggor_2896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 14
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EMSTEGGFGGTSSSDAQQSLQSFWP-RVMEEIRNLTVKDFRVQELP-LARIKKIMKLDEDVKMISAEAPV
          .MSTE.GF.GTSSS.AQ.SLQSFW.....EEI.NLTVKD..VQELP..A.IKKIMKL..DVKMIS.EAPV
Retrocopy KMSTECGFCGTSSSNAQ*SLQSFWA>HILEEIQNLTVKDLLVQELP<TAGIKKIMKLN-DVKMISREAPV

Parental  LFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVT
          LFAKAAQIFITELTL.A.IHTE..K..TL..ND..M.ITK.DQ.DFLIDIV..DEL.PPKRQEEV.QS.T
Retrocopy LFAKAAQIFITELTL*A*IHTEAKKHWTL*GNDVTMVITKLDQLDFLIDIVLTDELNPPKRQEEVCQSIT

Parental  PAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQ
          PA.P..YYFTLA.QP..V.V.GQQQGQ.TTSS.TTIQ.G.II..QPQQGQ..P.T.QVGEG.QVQIVQAQ
Retrocopy PAKPI*YYFTLA*QPSTVRV*GQQQGQETTSSMTTIQLG*IIM-QPQQGQIMPLTVQVGEGRQVQIVQAQ

Parental  PQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQI
          PQGQA.Q....TGQTM.VMQQIIT.TGEIQQIPVQL..GQL.YI.L.QPVSGTQV.Q.QI..LATNAQQI
Retrocopy PQGQA*QS*IDTGQTMEVMQQIITKTGEIQQIPVQLKLGQLEYILLVQPVSGTQVLQEQI*MLATNAQQI

Parental  TQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDGQAPQVTGD
          T.TEVQ.GQ.QF.Q.TDG..LYQIQQVT.P...DL.QPMF.QS.NQ.S..Q.PQVT.D
Retrocopy T*TEVQ*GQRQFNQVTDGHKLYQIQQVTIPVD*DLTQPMFNQSVNQLSYRQNPQVTHD

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	42.15 RPM
SRP007412_cerebellum	0.00 RPM	58.07 RPM
SRP007412_heart	0.00 RPM	26.89 RPM
SRP007412_kidney	0.00 RPM	43.22 RPM
SRP007412_liver	0.00 RPM	33.24 RPM
SRP007412_testis	0.00 RPM	38.33 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2896 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4668
Pan troglodytes	retro_ptro_3102
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	ENSGGOG00000004491	1 retrocopy	retro_ggor_1924,
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,