RetrogeneDB ID: retro_mmul_1202

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 15:95629766..95630498(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSMMUG00000014970
• Aliases: None
• Description: None

Sequence

>retro_mmul_1202
ATTATGAAACTGGATGAGGATGTGAAGATGATCAGTGCAGAGGCCCCTGTGCTCTTTGCCAGGGCGGCTCAGGTTTTTAT
CACGGAGTTGACTCTTCGAGCCTGGATTCACACACAGGATAACAAGTGCCAGACTCTATAGAGAAATGATATCCCCGTGG
AATTTGATCAATTTGCTTTTCTCCTCCATATTGTTCCAAGAGATGAACTGAAACCTCCAAAGTGTCAGGAGGAGGTGCTG
CAGTCTATAACTCCTGCTGAGCTAGTCCAGTACTATTTCACGCTGGCTCAGCAGCCCACCACCGTCCAAGTTCAGGGGCA
GCAGTAAGAGCAGCCCACTGCCAGCTCCATGACCACCATCCGGCCTGGGCAGCTCATCATCGCACAGCCTCAGCAGGGCC
AGACCACACCCGTGACAACACAGGTTGCAGAAGGTCAGCAGGTGCAGATTGTGCAGACCCAGCCACAGGGTCAAGCCCAA
TAGGCCCAGAGTGGCACTGGATGGTCCGTGCAGGTGACGCAGCAGATCCTCACTAACACAGGAGAGATCCAGCAGATCCC
AGTGCAGCTGAAAGCTGGCCAACTGCAGTGTATCTGCTTAGCCCAGTCTGTATCAGGCACCCAGGTTCTGCAGGGATAGA
TCCAGACACTTGACACCAACTCTCAACCGATTACACAGACAGAGGTCCAGCGAAGACAGCAGTAGTTCAGCCAGTTCACA
GGTGGACAGCAG

Alignment

ORF - retro_mmul_1202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 59.09 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPR
          IMKLDEDVKMISAEAPVLFA.AAQ.FITELTLRAWIHT.DNK..TL.RNDI......FDQF.FL..IVPR
Retrocopy IMKLDEDVKMISAEAPVLFARAAQVFITELTLRAWIHTQDNKCQTL*RNDIPV---EFDQFAFLLHIVPR

Parental  DELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTP
          DELKPPK.QEEV.QS.TPAE.VQYYFTLAQQPT.VQVQGQQ..Q.T.SS.TTI.PGQ.IIAQPQQGQTTP
Retrocopy DELKPPKCQEEVLQSITPAELVQYYFTLAQQPTTVQVQGQQ*EQPTASSMTTIRPGQLIIAQPQQGQTTP

Parental  VTMQVGEGQQVQIVQAQPQGQAQQAQSSTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGT
          VT.QV.EGQQVQIVQ.QPQGQAQ.AQS.TG...QV.QQI.TNTGEIQQIPVQL.AGQLQ.I.LAQ.VSGT
Retrocopy VTTQVAEGQQVQIVQTQPQGQAQ*AQSGTGWSVQVTQQILTNTGEIQQIPVQLKAGQLQCICLAQSVSGT

Parental  QVVQGQIQTLATNAQQITQTEVQQGQQQFSQFTDGQR
          QV.QG.IQTL.TN.Q.ITQTEVQ..QQ.FSQFT.GQ.
Retrocopy QVLQG*IQTLDTNSQPITQTEVQRRQQ*FSQFTGGQQ

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	0.11 RPM	22.75 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	32.76 RPM
SRP007412_cerebellum	0.00 RPM	26.48 RPM
SRP007412_heart	0.00 RPM	24.56 RPM
SRP007412_kidney	0.00 RPM	32.28 RPM
SRP007412_liver	0.00 RPM	25.14 RPM
SRP007412_testis	0.15 RPM	32.91 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1202 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1202 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1202 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4280
Pan troglodytes	retro_ptro_2903
Gorilla gorilla	retro_ggor_2865
Pongo abelii	retro_pabe_3490

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 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,