RetrogeneDB ID: retro_ggor_2865

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:69049483..69050491(-)
• 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_2865
GTCGAAATGTCCACAGAAGGAGGATTTGGTGGTACTAGCCGCAGTGATGCCCAGCAAAGCCTAAAGTCCTTCTGGTTTCG
GGTCATGGAAGAAATCTGGAATTTAGCAGTGAAAGATTTCTGAATGCAGGAACTCCCACTGGCTCGTATTAAGAAGATTA
TGAAACTGGATGAAGATGTGAAGATGATCAGTGCAGAGGCCCCTGTGCTCTTTGCCAGGGCAGCCCAGATTTTTTATCAC
AGAGTTGACTCTTCGAGCCTGGATTCACACAGAGGATAACAAGTGCCGGACTCTACAGAGAAATGATGTCGCCATGGCAA
TTACGAAATTTGATCAATTTGATTTTCTCATCGATATTGTTCTAAGAGATGAACTGAAACCTCCAAAGTGTCAGGAGGAG
GTGCTGCAGTCTGTAACTCCTGCTGAGCCAGTCCAATACTATTTCACGCTGGCTCAGCAGCCCACCGCCTTCCAAGTCCA
GGGACAGCAGCAAGGCCAGATCACCGCCAGCTCCATGACCACCATGCAGCCTGGGCAGATCACCATCGCACAGCTTCAGC
AGGGCCAGACCACGCCCGTGACGACGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGCCACAGGGTCAA
GCCCAGTAGGCCCAGAGTGGAACTGGATGGACCGTGCAGGTGATGTAGCAGATCCTCACTAACACAGGAGAGATCCAGAA
GATCCCGGTGCAGCTGAAGGCTGGCCAGCTGCAGTGTATCCACTTAGCCCAGTCTGCATCAGGCACCCAAGTTCTGCAGG
GACAGATCCAGACACTTGCCACCAGCGCTCAACCGATTACACAGACAAAGGTCCAGCAAAGACAACAGTAGTTCAGCCAG
TTCGCAGATGGAGAGCAGCTCTACCAGATCCAGCAAGTATCCATACCTGCGGGCCAGGACCTGCCCAGCCCATGTTTTTC
CAGTCAGTCAACCAGCCCTCTGATGGGCAGGCCCCCGGGGTGACTGGC

Alignment

ORF - retro_ggor_2865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.09 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEMSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVL
          VEMSTEGGFGGTS.SDAQQSL.SFW.RVMEEI.NL.VKDF..QELPLARIKKIMKLDEDVKMISAEAPVL
Retrocopy VEMSTEGGFGGTSRSDAQQSLKSFWFRVMEEIWNLAVKDF*MQELPLARIKKIMKLDEDVKMISAEAPVL

Parental  FAKAAQIF-ITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVT
          FA.AAQIF.ITELTLRAWIHTEDNK.RTLQRND.AMAITKFDQFDFLIDIV.RDELKPPK.QEEV.QSVT
Retrocopy FARAAQIF>ITELTLRAWIHTEDNKCRTLQRNDVAMAITKFDQFDFLIDIVLRDELKPPKCQEEVLQSVT

Parental  PAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQ
          PAEPVQYYFTLAQQPTA.QVQGQQQGQ.T.SS.TT.QPGQI.IAQ.QQGQTTPVT.QVGEGQQVQIVQAQ
Retrocopy PAEPVQYYFTLAQQPTAFQVQGQQQGQITASSMTTMQPGQITIAQLQQGQTTPVTTQVGEGQQVQIVQAQ

Parental  PQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQI
          PQGQAQ.AQSGTG.T.QVM.QI.TNTGEIQ.IPVQL.AGQLQ.I.LAQ..SGTQV.QGQIQTLAT.AQ.I
Retrocopy PQGQAQ*AQSGTGWTVQVM*QILTNTGEIQKIPVQLKAGQLQCIHLAQSASGTQVLQGQIQTLATSAQPI

Parental  TQTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDL-AQPMFIQSANQPSDGQAPQVTG
          TQT.VQQ.QQ.FSQF.DG.QLYQIQQV..PAGQDL.AQPMF.QS.NQPSDGQAP.VTG
Retrocopy TQTKVQQRQQ*FSQFADGEQLYQIQQVSIPAGQDL<AQPMFFQSVNQPSDGQAPGVTG

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_2865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2865 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4280
Pan troglodytes	retro_ptro_2903
Pongo abelii	retro_pabe_3490
Macaca mulatta	retro_mmul_1202

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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,