RetrogeneDB ID: retro_mmul_1218

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:19674410..19675563(+)
• Located in intron of: ENSMMUG00000018579

Retrocopy information

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

Parental gene information

• Parental gene symbol: KCTD9
• Ensembl ID: ENSMMUG00000010151
• Aliases: None
• Description: BTB/POZ domain-containing protein KCTD9 [Source:RefSeq peptide;Acc:NP_001247831]

Sequence

>retro_mmul_1218
ATGAGGTGGGTCACAGTGTTCCTGAACGGCAGCCCTGAGAACAGAAAGGTGGTTGCTGTGTATGGAACTTTATCGGATTT
GCTTTCTGTGGTCAGCAGTAAACTCAGCATAGAAGCCACCAGTGTGTATAATGGGAAAGGTGGGCTGATTGATGATATTG
CTTTGATCAGGGATGATGATGTTTTGTGTGTGGAGGAGAGCCGTTTATTGATCCTCAGACAGATTCTAAGCCACCTGAGG
GATTGTCAGGATTCCACACAGACTGGCTAACATTAAATGTTGGAGGGCAGTACTTTACAACCACACAGAGCACTTTAGCG
AATAAAGACCCTGACAGTATGCTGGCCCATGTGTTTAAGGACAAAGGTGTCTGGGAAATAAGCAAGATCATAGAGGAGCT
TTCTTAACTGACCGAAGTCCTGAGTACTTTGAACCCATTTTGAACTACTTGCGTCATGGATAGCTTATTGTAAATGATGG
CATTCATTTATTGGATGTGTTAGAAGAAGCAAGATTTTTTGGTATTTACTCATTGATTGAACACCTAGAAGTGGCAATAA
AGAATTCTCAACCACTGGAGGATTATTTACCAATATCCCGAAAGGAATTTGTCTGATTTTTGCTAGTAACTCCAACCAAG
TCAGAACTGCGATGCCAGGGTTTGAACTTCAGTGGTGCTGATCTTTCTCGTTTGGACCCTCGATACATTAACTTCAAAAC
GGCCAATTTAAGCTGCTGCAGTGTTGCACGTGCAAATCTTTGCTGTGTAAGTCTTGAACAAGCCGATCTCACTGGATCAG
TGCTTGACTGTGCAAATCTCCAGGGAGTCAAGATACTCTGTTCTAATGCAGAAGGAGCATCCCTGAAACTGTGTAATTTT
GAGGATCCTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAACCTCAAAAGTGTGGATATGGAAGGAAGTCACGTGACAGG
AATTAACCTGAGAGTGGCTACCTTAAAAAATGCAACGTTGAAGAACTGTAACCTCAGAGGAGCAACTCTGGCAGGAACTG
ATTTAGAGAATTGTGATCTATCTGGTTGTGATCTTCAAGAAGCCAAGGAGAGGGTCCAACATGAAAGGAGCTAGATTTGA
AGAGATGCTGACACCACTACACATGTCACAAAG

Alignment

ORF - retro_mmul_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 99.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVL-FVCEGEP
          MR.VT.FLNGSP.N.KVVAVYGTLSDLLSV.SSKL.I.ATSVYNGKGGLIDDIALIR.DD...FVC.GEP
Retrocopy MRWVTVFLNGSPENRKVVAVYGTLSDLLSVVSSKLSIEATSVYNGKGGLIDDIALIR-DDDV<FVCGGEP

Parental  FIDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRSTLVNKEPDSMLAHMFKDKGVW-GNKQDHRGAFLI
          FIDPQTDSKPPEGL.GFHTDWLTLNVGG.YFTTT.STL.NK.PDSMLAH.FKDKGVW.GNKQDHRGAFL.
Retrocopy FIDPQTDSKPPEGLSGFHTDWLTLNVGGQYFTTTQSTLANKDPDSMLAHVFKDKGVW<GNKQDHRGAFLT

Parental  DRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFVRF
          DRSPEYFEPILNYLRHG.LIVNDGI.LL.VLEEARFFGI.SLIEHLEVAIKNSQP.ED..PISRKEFV.F
Retrocopy DRSPEYFEPILNYLRHG*LIVNDGIHLLDVLEEARFFGIYSLIEHLEVAIKNSQPLEDYLPISRKEFV*F

Parental  LLATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQGV
          LL.TPTKSELRCQGLNFSGADLSRLD.RYINFK.ANLS.C..A.ANLCC..LE.ADL.GSVLDCANLQGV
Retrocopy LLVTPTKSELRCQGLNFSGADLSRLDPRYINFKTANLSCCSVARANLCCVSLEQADLTGSVLDCANLQGV

Parental  KMLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKNAKLKNCNLRGATLAGT
          K.LCSNAEGASLKLCNFEDPSGLKANLEGANLK.VDMEGS..TGINLRVATLKNA.LKNCNLRGATLAGT
Retrocopy KILCSNAEGASLKLCNFEDPSGLKANLEGANLKSVDMEGSHVTGINLRVATLKNATLKNCNLRGATLAGT

Parental  DLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQ
          DLENCDLSGCDLQEA..R.......I.....T..H...
Retrocopy DLENCDLSGCDLQEAKERVQHERS*I*RDADTTTHVTK

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	0.34 RPM	14.01 RPM
SRP007412_brain_prefrontal_cortex	0.16 RPM	7.06 RPM
SRP007412_cerebellum	0.26 RPM	22.28 RPM
SRP007412_heart	0.12 RPM	25.26 RPM
SRP007412_kidney	0.23 RPM	30.28 RPM
SRP007412_liver	0.00 RPM	4.71 RPM
SRP007412_testis	0.30 RPM	22.77 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1218 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1218 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2264

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Homo sapiens	ENSG00000104756	4 retrocopies	retro_hsap_1730, retro_hsap_3305, retro_hsap_4037, retro_hsap_4156,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309, retro_ggor_2264, retro_ggor_2791,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218 , retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,
Pan troglodytes	ENSPTRG00000020092	3 retrocopies	retro_ptro_1225, retro_ptro_2166, retro_ptro_2825,