RetrogeneDB ID: retro_mmul_246

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:93532010..93533582(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000023376
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KDM4B
• Ensembl ID: ENSMMUG00000012677
• Aliases: KDM4B, JMJD2B
• Description: lysine-specific demethylase 4B [Source:RefSeq peptide;Acc:NP_001253377]

Sequence

>retro_mmul_246
ATGGAAACTATGAAGTCTAAGGCCAACTATGGCCAGAATCCAAATTGTAACATAATGATATTTCATCCAACCAAAGAAGA
GTTTAATGATTTTGATAAATATATTGCTTACATGGAATCCCAAGGTGCACACAGAGCTGGCTTGGCTAAGATAGTTCCAC
CCAAAGAATGGAAAGCCAGAGAGACCTATGATAACATCAGTGAAATCTTAATAGCCACTCCCCTCCAACAGGTGGCCTCT
GGGCGGGCAGGGGTGTTTACTCAATACCATAAAAAAAAGAAAGCCATGACCGTGGGGGAGTATCGCCACTTGGCAAACAG
TAAAAAATATCAAACTCCACCACACCAGAATTTCGAAGATTTGGAGCGAAAATACTGGAAGAACCGCATCTATAATTCAC
CAATTTATGGTGCTGACATCAGTGGCTCCTTGTTTGATGAAAACACTAAACAGTGGAATCTTGGGCACCTGGGAACAATT
CAGGACCTGTTGGAAAAGGAATGTGGGGTTGTCATAGAAGGCGTTAACACACCCTACTTGTACTTTGGCATGTGGAAGAC
CACATTTGCTTGGCACACGGAGGACATGGACCTTTACAGCATCAACTACCTGCACCTCGGGGAGCCCAAAACTTGGTATG
TGGTGCCCCCAGAGCATGGCCAGCGCCTGGAACGCCTGGCCAGGGAGCTCTTCCCAGGCAGTTCCCGGGGCTGTGGGGCC
TTCCTGCGGCACAAGGTGGCCCTCATCTCGCCTACAGTTCTCAAGGAAAATGGGATCCCCTTCAATCGCATAACTCAGGA
GGCTGGAGAGTTCATGGTGACCTTTCCCTATGGCTACCATGCTGGCTTCAACCATGGTTTCAACTGTGCAGAGGCCATCA
ATTTTGCCACTCCACGATGGATTGATTATGGCAAAATGGCCTCCCAGTGTAGCTGTGGGGAGGCCAGGGTGACCTTTTCC
ATGGACGCCTTCGTGCGCATCCTGCAACCTGAGCGCTATGAGCTGTGGAAACGTGGGCAAGACCGGGCAGTTGTGGACCA
CATGGAGCCCAGGGTACCAGCCAGCCAAGAGCTGAGCACCCAGAAGGAGGTCCAGTTGCCCAGGAGAGCAGCGCTGGGCC
TGAGACAACTCCCTCCTCACTGGGCCCGGCATTCCCCTTGGCCTCTGGCTGCCCGCAGTGGGACGCGCTGCCACACCCTT
GTGTGCTCTTCACTCCCACGCCGATCTGCAGTTAGTGGCACTGCTACGCAGCCCCGGGCTGCTGCCGTCCACAGCTCTAG
GAAGCCCAGCTCAACTCCATCATCCACCCCTGGTCCATCTGCACAGATTATCCACCCGTCAAATGGCAGACGTGGACGTG
GTCGCCGTCCTCAGAAACTGAGAGCTCAGGAGCTGACCCTCCAGACTCCAGCCAAGAGGCTCCTCTTAGCGGGCACAACA
TGCACAGTTTCAGGCCCAGAACCTGAGCCCCTACCTGAGGGTGGGGCTTTGATGGACAAGCCTGTACCACTGAATCCAGG
GCTCCAGCATCCTGTAAAGGCTTCTAGGTGCAGCTGGGCCCCTGTGCCCTAA

Alignment

ORF - retro_mmul_246 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.51 %
• Parental protein coverage: 87.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSEDHGAQNPSCKIMTFRPTMEEFKDFNKYVAYIESQGAHRAGLAKIIPPKEWKPRQTYDDIDDVVIPA
          M.S.....QNP.C.IM.F.PT.EEF.DF.KY.AY.ESQGAHRAGLAKI.PPKEWK.R.TYD.I....I..
Retrocopy MKSKANYGQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIVPPKEWKARETYDNISEILIAT

Parental  PIQQVVTGQSGLFTQYNIQKKAMTVGEYRRLANSEKYCTPRHQDFDDLERKYWKNLTFVSPIYGADISGS
          P.QQV..G..G.FTQY...KKAMTVGEYR.LANS.KY.TP.HQ.F.DLERKYWKN....SPIYGADISGS
Retrocopy PLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGS

Parental  LYDDDVAQWNIGSLRTILDMVERECGTIIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWY
          L.D....QWN.G.L.TI.D..E.ECG..IEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLH.GEPK.WY
Retrocopy LFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWY

Parental  AIPPEHGKRLERLAIGFFPGSSQGCDAFLRHKMTLISPIILKKYGIPFSRITQEAGEFMITFPYGYHAGF
          ..PPEHG.RLERLA...FPGSS.GC.AFLRHK..LISP..LK..GIPF.RITQEAGEFM.TFPYGYHAGF
Retrocopy VVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGF

Parental  NHGFNCAESTNFATLRWIDYGKVATQCTCRKDMVKISMDVFVRILQPERYELWKQGKDLTVLDHTRPTAL
          NHGFNCAE..NFAT.RWIDYGK.A.QC.C....V..SMD.FVRILQPERYELWK.G.D..V.DH..P...
Retrocopy NHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYELWKRGQDRAVVDHMEPRVP

Parental  TSPELSSWSASRASLKAKL-LRR-TPFCASVSPLPHRPQPGVWC
          .S.ELS..........A.L.LR...P..A..SP.P.....G..C
Retrocopy ASQELSTQKEVQLPRRAALGLRQLPPHWARHSPWPLAARSGTRC

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	0.45 RPM	19.27 RPM
SRP007412_brain_prefrontal_cortex	0.71 RPM	62.04 RPM
SRP007412_cerebellum	1.03 RPM	23.12 RPM
SRP007412_heart	0.65 RPM	21.02 RPM
SRP007412_kidney	0.23 RPM	19.72 RPM
SRP007412_liver	0.28 RPM	23.20 RPM
SRP007412_testis	218.28 RPM	25.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_246 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000012677	1 retrocopy	retro_mmul_246 ,