RetrogeneDB ID: retro_mmul_35

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:30853273..30855586(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016517
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UTP14A
• Ensembl ID: ENSMMUG00000020700
• Aliases: None
• Description: None

Sequence

>retro_mmul_35
ATGAATGTGAACCGGGTTGCGGAGAGCCTTCTGGCTTTGAGCCAACAGGAAGAATTAGTGGATTTGCCAAAAAACTGCCC
CTTGAGTGAGAATGAAGATGAGGGGGACAGTGATGGAGAGAGAAAGCATCAAAAGCTTCTGGAAGCAATCAGTTCCCTTG
ATGGAAAGAATAGGCGGAAATTGGCTGAGAGGTCTGAGGCTAGTCTGAAAGTGTCAGAGTTCAATGTCAGTTCTGAAGGA
TCAGGAGAAAAGCTGGTCCTTGCAGATCTCCTTGAGCCTGTTAAAACTACTTCTTCTTTGGCCACTGTGAAAAAGCAACT
GAATAGAGTCAAATCAAAGAAGGTGGTGGAGTTACCTCTTAACAAAGAAAAGATTGAACAGATCCACAGAGAAGTAGCAT
TCGGTAAAACCTCACAAGTCCTCTCTAAATGGGACCCTATCGTCCTGAAGAACCAGCAGGCAGAGCAGCTGGCTTTTCCC
CTGGGGAAGGAGCAGCCAGCCATTGCTCCCATTGAACATGCGCTCAGTGGCTGGAAGGCAAGAACTCCCCTGGAGCAGGA
AATTTTTAACCTCCTCCATAAGAACAAGCAGCCAGTAACAGACCCTTTACTGACTCCCATGGAAAAGGCCTCTCTCCGAG
CCATGAGTCTGGAAGAGGCAAAGATGCACCGAGCAGAGCTTCAAAGGGCTCGGGCTCTGCAGTCCTACTATGAGGCCAAG
GCTCGAAGAGAGAAGAAAATCAAAAGTAAAAAGTATCACAAAGTCGTGAAGAAAGGAAAGGCCAGGAAAGTCTCAAAAGA
GTTGGAGCAGCTGCAGAAGGTTAATCCAACTGTGGCATTGGAAGAACTGGAAAAATTTGAAAATGCCAGAATGATGGAAA
GAATGAGCCTTAAGCACCAAAACAGTGGGAAATGGGCCAAGTCAAAGGCAATTATGGCAAAATATGACCTGGAGGCTCGC
CAAGCTATGCAGGAACAGTTGGCCAAGAACAAAGAACTGACACAGAAACTCCAGGTAGCCTCTGAGATTGAGGAAGAGGA
GGGAGGCACAGAAGAAGTGGAAGAACTCCTTGTCCCCCATGTAGTGAATGAAGTCCAGATGAATGTGGAAGGACCGAATC
CCTGGATGCTCAGAAGCTGCACCAGTGACACCAGAGAGGCTGCAACCCAGGAGGACCCTGAGCAACTGCCAGAGCCTGCG
ACCCATGAGGTTTCTGAAAGTGAGGGAGAAAGACCAGTGGCAGAGGAAGAAATTTTGTTGAGAGACTTTGAGGAGAGGCG
ATCCCTTAGAAAAAGATCTGAGCTCAACCAGGATGCTGAGCCAGCAGGCATTCAAGAAACAAAAGATTCTAGCAGCCAGG
AGGTGCTGTCTGAATTGAGGGCACTATCTCAGAAATTGAAGGAAAACCATCAGTCCAGGAAGCAAAAAGCAAGTTCAGAG
GGGACTGTTCCCCAGGTCCAGAGAGAGGAACCTGCCCCAGAAGAAGAGGCGCCCCTGTTGCTACAGAGGCCAGAGAGAGT
ACAAACTGTGGAAGAGCTAGAAGAGCTGGGAAAAGAAGATTGTTTTCAAAATAAGGAGCTTCCCAGACCTGTGTTAGAAG
GGCAGCAGTCAGAGAGGACCCCAAATAATCGGCCTGATGCCCCTAAGGAGAAGAAAGAGAAGGAGCAACTGATCAACGTA
CAGAACTTCCTAACTACACAGTCTCCTTCCGTGAGGTCTTTGGCAGTTCCCACAACAATAGAGGAGCTGGAAGATGAAGA
GGAGAGAGACCAAAGGCAGATGATAAAGGAAGCTTTTGCTGGGGATGATGTCATCAGAAATTTCTTGAAAGAGAAGAGAG
AAGCTGTGGAGGCGAGTAAGCCAAAGGACGTGGACCTGACACTACCTGGCTGGGGCGAGTGGGGTGGTGTGGGCCTAAAG
CCTAGTACCAAGAAAAGACGCCAGTTTCTCAAAGCCCCTGAGGGTCCTCCAAGAAAAGATAAGAATTTGCCAAATGTGAT
TATCAGTGAGAAGCGCAACATCCACGCAGCAGCTCATCAGGTACAAGTGCTTCCATATCCATTTACCCACCATCGGCAAT
TTGAAAGGACCATCCAGACCCCTGTAGGATCCACATGGAACACCCAGAGGGCTTTCCAAAAGCTGACTACTCCCAAGGTC
ATCACCAAGCCAGGTCATATCATTAAGCCCATAAAAGCAGAGGATGTGGGCTACCGGTCTTCCTCAAGGTCAGACCTGTC
TGTCATACAGTGGAATCCAAAACAAATCACCACACGTCACAGTAAAGAGTTGAAGAAAAACTCTGTAGGTTGA

Alignment

ORF - retro_mmul_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.49 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTANRLAESLLALSQQEELVDLPKDYLLSGSEDEGDNDGEREHQKLLEAISSLDGKNRRKLAERSEASLK
          M..NR.AESLLALSQQEELVDLPK...LS..EDEGD.DGER.HQKLLEAISSLDGKNRRKLAERSEASLK
Retrocopy MNVNRVAESLLALSQQEELVDLPKNCPLSENEDEGDSDGERKHQKLLEAISSLDGKNRRKLAERSEASLK

Parental  VSEFNVSSEGSGEKLVLADLLEPVKTSSSLATVKKQLNRVKSKKTVELPLNKEEIERIHREVAFNKTAKV
          VSEFNVSSEGSGEKLVLADLLEPVKT.SSLATVKKQLNRVKSKK.VELPLNKE.IE.IHREVAF.KT..V
Retrocopy VSEFNVSSEGSGEKLVLADLLEPVKTTSSLATVKKQLNRVKSKKVVELPLNKEKIEQIHREVAFGKTSQV

Parental  LSKWDPVVLKNRQAEQLVFPLEKEEPAIAPIEHVLSGWKARTPLEQEIFNLLHKNKQPVADPLLTPVEKA
          LSKWDP.VLKN.QAEQL.FPL.KE.PAIAPIEH.LSGWKARTPLEQEIFNLLHKNKQPV.DPLLTP.EKA
Retrocopy LSKWDPIVLKNQQAEQLAFPLGKEQPAIAPIEHALSGWKARTPLEQEIFNLLHKNKQPVTDPLLTPMEKA

Parental  SLQAMSLEEAKMRRAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKAKKALKEFEQLRKVNPAAAL
          SL.AMSLEEAKM.RAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKA.K..KE.EQL.KVNP..AL
Retrocopy SLRAMSLEEAKMHRAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKARKVSKELEQLQKVNPTVAL

Parental  EELEKIEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVASESEEEEGGT
          EELEK.E.ARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVASE.EEEEGGT
Retrocopy EELEKFENARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVASEIEEEEGGT

Parental  EEKVEELLVPDVVNEVQMNADGPNPWMLRSCTSDTKEAATQEDPEQLPEPEAHEVSESEGEDRPVAEEEI
          EE.VEELLVP.VVNEVQMN..GPNPWMLRSCTSDT.EAATQEDPEQLPEP..HEVSESEGE.RPVAEEEI
Retrocopy EE-VEELLVPHVVNEVQMNVEGPNPWMLRSCTSDTREAATQEDPEQLPEPATHEVSESEGE-RPVAEEEI

Parental  LLREFEERRSLRKRSELSQDAEPAGSQETKDSSSQEVLSELRVLSQKLKENDQSRKQKASSEGTIPQVQR
          LLR.FEERRSLRKRSEL.QDAEPAG.QETKDSSSQEVLSELR.LSQKLKEN.QSRKQKASSEGT.PQVQR
Retrocopy LLRDFEERRSLRKRSELNQDAEPAGIQETKDSSSQEVLSELRALSQKLKENHQSRKQKASSEGTVPQVQR

Parental  EEPATEEEEPLLLQRPERVQTLEELEELGKEECFQNKELSRPVLEGQQSERTPNNRPDAPK-KKKKEQMI
          EEPA.EEE.PLLLQRPERVQT.EELEELGKE.CFQNKEL.RPVLEGQQSERTPNNRPDAPK.KK.KEQ.I
Retrocopy EEPAPEEEAPLLLQRPERVQTVEELEELGKEDCFQNKELPRPVLEGQQSERTPNNRPDAPKEKKEKEQLI

Parental  DLQNLLTTQSPSVKSLAVP-TIEELEDEEERNQRQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTL
          ..QN.LTTQSPSV.SLAVP.TIEELEDEEER.QRQMIKEAFAGDDVIR.FLKEKREAVEASKPKDVDLTL
Retrocopy NVQNFLTTQSPSVRSLAVPTTIEELEDEEERDQRQMIKEAFAGDDVIRNFLKEKREAVEASKPKDVDLTL

Parental  PGWGEWGGVGLKPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNIHTAAHQVR
          PGWGEWGGVGLKPS.KKRR.FL.KAPEGPPRKDKNLPNVII.EKRNIH.AAHQV.
Retrocopy PGWGEWGGVGLKPSTKKRRQFL-KAPEGPPRKDKNLPNVIISEKRNIHAAAHQVQ

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	29.13 RPM	5.83 RPM
SRP007412_brain_prefrontal_cortex	25.70 RPM	7.62 RPM
SRP007412_cerebellum	34.87 RPM	8.07 RPM
SRP007412_heart	11.13 RPM	6.95 RPM
SRP007412_kidney	25.47 RPM	5.52 RPM
SRP007412_liver	10.33 RPM	1.62 RPM
SRP007412_testis	6.75 RPM	0.87 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_35 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_35 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35 ,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,