RetrogeneDB ID: retro_mmul_1725

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:133598660..133599337(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSMMUG00000014944
• Aliases: None
• Description: UV excision repair protein RAD23 homolog B [Source:RefSeq peptide;Acc:NP_001248717]

Sequence

>retro_mmul_1725
ATGGTGATAAAACCCAAAGAGTGACAATACCAGTTCCAGCTACAATGCAGCAATCAAATCCTGCCACCACTATGAAGTGA
GTTCCTCCACAGCAGCTGCTGTGGCTCAGGCTGCAACCCTCATCTCTGCCTTGGCTCCCACATCCACACCTGCATCTATC
ATCCCACCAACAACGCCATGTCCTGAACATGTACCTTCTAGTGCAATGAAACAAGATAAACCTGCAGAAAAGTCAGCAGA
AATACCAGTGGCTACTAGTTCAACATTAACTGAGAGTAGAGCAGTGGATTCTTCTCTGCCAAACCTTGTTGAAGTTGCAA
ATGCACTTGTAAAAAGTCAGTCCTATGAGAATATGGTAACTGAGATCATGTCAATGGGCTATAAACAAGAGCAAGAAATT
GTGTCCCTGAGAGCCGTTTTCAACAATCCTGACAGAGCAGTGCAGTATCTTTTAATAGGAATCCCTGGAGGTAGAAAAAG
TCAGGCTGTGGTTGAGCACCTCCCCCCACCCCCAATCAGGTACTACTAGGACCCCTCAGTCTTCAGCAGTGTCTTCAGCT
GCTGCAACTATGACAGCAACAACTACAAGTTCTGGGGAACATCCCCATGAAATTTTATAGAATCAGCCTCAGTTTTGACA
GATGAGACAAATTACTCAATAGAGTCCTTCCCTGCTT

Alignment

ORF - retro_mmul_1725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.24 %
• Parental protein coverage: 55.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVTKPKA-VSTPAPATTQQSAPASTTA-ITSSTATTVAQAPTPVPALAPTSTPASITPASATASSEPAPA
          MV.KPK..V..P.PAT.QQS.PA.T.....SSTA..VAQA.T...ALAPTSTPASI.P...T...E..P.
Retrocopy MVIKPKE<VTIPVPATMQQSNPATTMK<VSSSTAAAVAQAATLISALAPTSTPASIIPPT-TPCPEHVPS

Parental  SATKQEKPAEKPAETPVATSPTATDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIAA
          SA.KQ.KPAEK.AE.PVATS.T.T.S...DSS..NL.E.A..ALV..QSYENMVTEIMSMGY..EQ.I..
Retrocopy SAMKQDKPAEKSAEIPVATSSTLTESRAVDSSLPNLVEVA-NALVKSQSYENMVTEIMSMGYKQEQEIVS

Parental  LRASFNNPDRAVEYLLMGIPGDRESQAVVD---PP-QAASTGAPQSSAVAAAAATTTATTTTTSSGGHPL
          LRA.FNNPDRAV.YLL.GIPG.R.SQAVV....PP.Q...T..PQSSAV..AAAT.TA..TTTSSG.HP.
Retrocopy LRAVFNNPDRAVQYLLIGIPGGRKSQAVVEHLPPP>QSGTTRTPQSSAVSSAAATMTA--TTTSSGEHPH

Parental  EFLRNQPQFQQMRQIIQQNPSLL
          E.L.NQPQF.QMRQI.Q..PSLL
Retrocopy EIL*NQPQF*QMRQITQ*SPSLL

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	0.00 RPM	126.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	106.78 RPM
SRP007412_cerebellum	0.00 RPM	119.66 RPM
SRP007412_heart	0.00 RPM	88.09 RPM
SRP007412_kidney	0.00 RPM	83.68 RPM
SRP007412_liver	0.00 RPM	74.93 RPM
SRP007412_testis	0.00 RPM	78.52 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1725 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1725 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3754
Pongo abelii	retro_pabe_3162

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725 ,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,