RetrogeneDB ID: retro_mmul_683

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214515947:1841..3200(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2129
• Ensembl ID: ENSMMUG00000018287
• Aliases: None
• Description: cytochrome b-c1 complex subunit 2, mitochondrial [Source:RefSeq peptide;Acc:NP_001248062]

Sequence

>retro_mmul_683
ATGAAGCTACTAACCAAAGCTGGGTCCTTCTCGAGATTTTATTCCCTCAAAGTTTCCCCCAAAGTTAAAGCCACAGCTGC
GCCTGCAGGAGCACCACCACAACCTCAGGACCTTGAGTTTACCAAGTTACCAAATGGCTTGGTGATTGCTTCTTTGGAAA
ACTATGCTCCTCTATCAAGAATTCTTTTGTTCATTAAAGCAGGCAGTAGATATGAGGACTCCAACAATTTAAGAACCACC
CATTTGCTGCAACTTGCATCCAGTCTGACAACACAAGTAGCTTCATTTTTCAAGATTACCCATGGAATTGAAGCAACTGG
TGGCAAATTAAGTGTGGCTGCAACAAAGGAAACCATGGCTTACACTGTGGAATGCCTGTGAGGTGATGTTGATATTCTAA
TGGAGTTCCTGCTCAATGTCACCACAGCACCAGAATTTCGTCGTTGGGAAGTAGCTGACCTTCAGCCTCAGCTAAAGATT
GACAAAGCTGTGGCCTTTCAGAATCCACAGACTCATGTCATTGAAAATTTGCATGCAGCAGCTTACCGGAATGCCTTGGC
TAATCCCTTGTACTGTCCTGACTATAGAATTGGAAAAGTGACATCAGAGGAGTTACATTACTTTGTTCAGAACCATTTCA
CAAGTGCAAGAATGGCTTTGATTGGACTTGGCGTGAGTCATCCTGTTTTAAAGCAAGTTGCTGAACAGTTTCTCAACATG
AGGGGTGGGTTTGGTTTATCTGGTGTGAAGGCCAAATACCGTGGAGGTGAAATCCGAGAACAGAATGGAGACAGTCTTGT
CCATGCTGCTCTTGTAGCCGAAAGTGCTGTCACGGGAAGTGTAGAGGCAAATGCGTTTAGTAACCTTCAGCATGTCCTTG
GTGCCAGGCCACATGTCAAGAGGGGCAGCAGCCCCACCAGCCATCTACACCAAGCTGTTGCCAAGGCAACTCAGCAGCCA
ATTGATGTTTCCGCATTTAATGCCAGTTACTCAGATTCTGGACTCTTCGGGATTTATACTATCTCCCAGGCCACAGCTGC
TGGAGATGTAATCAAGGCTGCGTAGAATCAAGTCAAAACAATAGCTCAAGGAAACCTTTCCAACACAGATGTCCAAGCTG
CCAAGAACAAGCGGAAAGCTGGATACCTAATGTCAGTGGAGTCTTCTGAGCGTTTCTTGGAAGAAGACGGGTCCCAGGCT
CTAATTGCTGGTTCTTATGTGCCACCATCCACAGTCCTTCAGCAGATTGATTCAGTGGCTAATGCTGATATCATAAATGC
TGCAAAGAAGTTTGTTTCTGGCCAGAAGTCAATGGCAGCAAGTGGAAATTTGGGACGTACACCTTTTGTTGATGAGCTG

Alignment

ORF - retro_mmul_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKLLTRAGSFSRFYSLKVAPKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYAPLSRIGLFIKAGSR
          MKLLT.AGSFSRFYSLKV.PKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYAPLSRI.LFIKAGSR
Retrocopy MKLLTKAGSFSRFYSLKVSPKVKATAAPAGAPPQPQDLEFTKLPNGLVIASLENYAPLSRILLFIKAGSR

Parental  YEDSNNLGTTHLLRLASSLTTKGASSFKITHGIEAVGGKLSVTATRETMAYTVECQRGDVDILMEFLLNV
          YEDSNNL.TTHLL.LASSLTT..AS.FKITHGIEA.GGKLSV.AT.ETMAYTVEC..GDVDILMEFLLNV
Retrocopy YEDSNNLRTTHLLQLASSLTTQVASFFKITHGIEATGGKLSVAATKETMAYTVECL*GDVDILMEFLLNV

Parental  TTAPEFRRWEVADLQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYFVQ
          TTAPEFRRWEVADLQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYFVQ
Retrocopy TTAPEFRRWEVADLQPQLKIDKAVAFQNPQTHVIENLHAAAYRNALANPLYCPDYRIGKVTSEELHYFVQ

Parental  NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGFGLSGVKAKYRGGEIREQNGDSLVHAALVAESAVAGS
          NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGFGLSGVKAKYRGGEIREQNGDSLVHAALVAESAV.GS
Retrocopy NHFTSARMALIGLGVSHPVLKQVAEQFLNMRGGFGLSGVKAKYRGGEIREQNGDSLVHAALVAESAVTGS

Parental  AEANAFSVLQHVLGAGPHVKRGSNTTSHLHQAVAKATQQPFDVSAFNASYSDSGLFGIYTISQATAAGDV
          .EANAFS.LQHVLGA.PHVKRGS..TSHLHQAVAKATQQP.DVSAFNASYSDSGLFGIYTISQATAAGDV
Retrocopy VEANAFSNLQHVLGARPHVKRGSSPTSHLHQAVAKATQQPIDVSAFNASYSDSGLFGIYTISQATAAGDV

Parental  IKAAYNQVKTIAQGNLSNTDVQAAKNKLKAGYLMSVESSERFLEEVGSQALVAGSYVPPSTVLQQIDSVA
          IKAA.NQVKTIAQGNLSNTDVQAAKNK.KAGYLMSVESSERFLEE.GSQAL.AGSYVPPSTVLQQIDSVA
Retrocopy IKAA*NQVKTIAQGNLSNTDVQAAKNKRKAGYLMSVESSERFLEEDGSQALIAGSYVPPSTVLQQIDSVA

Parental  NADIINAAKKFVSGQKSMAASGNLGHTPFVDEL
          NADIINAAKKFVSGQKSMAASGNLG.TPFVDEL
Retrocopy NADIINAAKKFVSGQKSMAASGNLGRTPFVDEL

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	0.22 RPM	166.06 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	139.70 RPM
SRP007412_cerebellum	0.19 RPM	142.32 RPM
SRP007412_heart	1.65 RPM	310.33 RPM
SRP007412_kidney	0.23 RPM	222.88 RPM
SRP007412_liver	0.00 RPM	120.49 RPM
SRP007412_testis	0.26 RPM	85.38 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_683 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Homo sapiens	ENSG00000140740	1 retrocopy	retro_hsap_2785,
Gorilla gorilla	ENSGGOG00000015379	1 retrocopy	retro_ggor_1941,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Macaca mulatta	ENSMMUG00000018287	2 retrocopies	retro_mmul_1442, retro_mmul_683 ,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Nomascus leucogenys	ENSNLEG00000012185	1 retrocopy	retro_nleu_685,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Pongo abelii	ENSPPYG00000007174	1 retrocopy	retro_pabe_2232,
Pan troglodytes	ENSPTRG00000007871	1 retrocopy	retro_ptro_1886,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,