RetrogeneDB ID: retro_mmul_1808

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:155107789..155108945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF259
• Ensembl ID: ENSMMUG00000020287
• Aliases: None
• Description: None

Sequence

>retro_mmul_1808
ATCGTGAGCTCCTTTTCCTGCCACCACTGTGGCTGGAACAACACAGAGATCCGGTCGGCAGGCAGGAGCCAGGACCAGGG
AGTGCGCTACACTCGGACCTTCAGGGCTCTGTAGGACATGACAGAGAAACAGTGAAGACTGACTCTGCTACCACAAGGAT
TCCTGAGCTAGATTTTCAAATTCCTGCCCTTAGCCAGAAAGGAGCTCTGTCCGCTGTTGAAGGATTGATCACCCATTGCT
ATCTCTGGCCTGGAGCAGGACCAGCCTGCACGAAGGGCAAACAAAGATGCCACAGCTGAAAGAATTGATGAGTTCGTTGT
CAAACCGGAGGAGCTGAAGCAAGCAGTCTCCCCTTTCACTCTGATCATTGATGATCCCTCAGGGAACAGCTCCGTGGAAA
ACCCACGTGCTGCTCAGAAAGATGATGCCCTGGTGATCACACACTACAACTGGACCCGACAGCAGAAAGAGATGCTGGGG
CTCCAGGCAGAGCACCCACAGAGAAGCCAGAGGAGGAAGATGTCAGAAATGAAGTGCTCCAGTTTAACACAAACGGCCCA
GAATGAAATGCCCCCGCTCAGACCAACATGAAGCTAGTACAAATCCCTCCCTTTAAGGAGGTTATCATCATGGCTACTAA
CTGCAAGAACTGTAGGCATCACACCAGTGAGGTGAAATCTGGAGAAGCAGTAGAATCCTTGGGCACCAGGATCACCCTCC
ACATCACAGTTCCCTCAGATATGATCAGAGACCTCCTCAAGTGTGAGGTTTGTAGTGTGGAAATCCCAGAGCTAGAATTT
GACTGGGAGTGGCCATCCTCGGGGGCAAGTTCATCACATTGGAAGGGCCACTGAAAGATATGTGGGAACTGGTGACCAAA
AGCCCTTTCACACTGGGCGACAGTTCCAATCCTGGCCAGACGGAGAGACTGCAGGAGTTTAGCCAGAAGATGGACCAGAT
CATTGAAGGTAACACGAAGACCCACTTTATTATGGATGATCCAGCAGGAAACAGTTACTTGTAAAACGTGTATGCACCTG
AAGATGATCCTGAGATGAAGGTGGAGCATTACAAGCGCACCTCTGACCAAAATGAGGAGCTAGAGCTCAGTGACATAAAG
ACAGAGGGCTATAAGGCAGGCCTGGCTCCACAACAG

Alignment

ORF - retro_mmul_1808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 84.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IVSSF-CEHCGWN-TEIQSAGR-QDQGVRYTLTVRAPEDM-NREVVKTDSATTRIPELDFEIPAFSQKGA
          IVSSF.C.HCGWN.TEI.SAGR.QDQGVRYT.T.RA..DM..RE.VKTDSATTRIPELDF.IPA.SQKGA
Retrocopy IVSSFSCHHCGWNNTEIRSAGRSQDQGVRYTRTFRAL*DM<DRETVKTDSATTRIPELDFQIPALSQKGA

Parental  LTTVEGLITR-AISGLEQDQPARRANKDATAERIDEFIVKLKELKQVASPFTLIIDDPSGNSFVENPHAP
          L..VEGLIT..AISGLEQDQPARRANKDATAERIDEF.VK..ELKQ..SPFTLIIDDPSGNS.VENP.A.
Retrocopy LSAVEGLITH>AISGLEQDQPARRANKDATAERIDEFVVKPEELKQAVSPFTLIIDDPSGNSSVENPRAA

Parental  QKDDSLVITHYNRTQHQKEMLGLQEE-APAEKPEEEDLRNEVLQFNTNCPECNAPAQTNMKLVQIPHFKE
          QKDD.LVITHYN.T..QKEMLGLQ.E.AP.EKPEEED.RNEVLQFNTN.PE.NAPAQTNMKLVQIP.FKE
Retrocopy QKDDALVITHYNWTRQQKEMLGLQAE<APTEKPEEEDVRNEVLQFNTNGPE*NAPAQTNMKLVQIPPFKE

Parental  VIIMATNCENCGHRTNEVKSGGAVEPLGTRITLHITDPSDMTRDLLKSETCSVEIPELEFE-LGMAVLGG
          VIIMATNC.NC.H.T.EVKSG.AVE.LGTRITLHIT.PSDM.RDLLK.E.CSVEIPELEF..LG.A.LGG
Retrocopy VIIMATNCKNCRHHTSEVKSGEAVESLGTRITLHITVPSDMIRDLLKCEVCSVEIPELEFD<LGVAILGG

Parental  KFTTLEGLLKDIRELVTKNPFTLGDSSNPCQKERLQEFSQKMDQIIEGNMKAHFIMDDPAGNSYLQNVYA
          KF.TLEG.LKD..ELVTK.PFTLGDSSNP.Q.ERLQEFSQKMDQIIEGN.K.HFIMDDPAGNSYL.NVYA
Retrocopy KFITLEGPLKDMWELVTKSPFTLGDSSNPGQTERLQEFSQKMDQIIEGNTKTHFIMDDPAGNSYL*NVYA

Parental  PEDDPEMKVERYKRTFDQNEELGLNDMKTEGYEAGLASQR
          PEDDPEMKVE.YKRT.DQNEEL.L.D.KTEGY.AGLA.Q.
Retrocopy PEDDPEMKVEHYKRTSDQNEELELSDIKTEGYKAGLAPQQ

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	34.06 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	33.08 RPM
SRP007412_cerebellum	1.03 RPM	26.73 RPM
SRP007412_heart	0.00 RPM	15.07 RPM
SRP007412_kidney	0.00 RPM	29.81 RPM
SRP007412_liver	0.00 RPM	23.20 RPM
SRP007412_testis	0.11 RPM	99.93 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1808 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1808 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1808 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011907	1 retrocopy	retro_etel_246,
Homo sapiens	ENSG00000109917	1 retrocopy	retro_hsap_3639,
Gorilla gorilla	ENSGGOG00000000664	1 retrocopy	retro_ggor_2455,
Myotis lucifugus	ENSMLUG00000014012	1 retrocopy	retro_mluc_2167,
Macaca mulatta	ENSMMUG00000020287	1 retrocopy	retro_mmul_1808 ,
Mus musculus	ENSMUSG00000032078	2 retrocopies	retro_mmus_3602, retro_mmus_3701,
Otolemur garnettii	ENSOGAG00000009977	1 retrocopy	retro_ogar_506,
Pongo abelii	ENSPPYG00000025914	1 retrocopy	retro_pabe_2986,
Pan troglodytes	ENSPTRG00000004312	1 retrocopy	retro_ptro_2464,
Sus scrofa	ENSSSCG00000015066	1 retrocopy	retro_sscr_1150,