RetrogeneDB ID: retro_mmul_1329

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 18:25430593..25431656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4373
• Ensembl ID: ENSMMUG00000019299
• Aliases: None
• Description: WW domain-binding protein 11 [Source:RefSeq peptide;Acc:NP_001244865]

Sequence

>retro_mmul_1329
AAATAGCTGCGTGAAACCTTTGAACATATTCTACGACTCTATGACAAAGAGAATCCAGATATTTAGAAAGAATTGAGAAA
GCTAGAAATAGATTATGAACAGAAGAGGGCTCAACTTAATCAATATTTGGATGCTGTGGAGCATGCTCAGCATGTGGAAG
TGGAGAGTATTCCTTTGCCAGATATGCCGCAGGCTCCTTCTAACATTTGGATCCAGGACATTCCACTTCCTGGTGTCCAG
TCACCCTCCATCCTTAAGAAACCCTCAGCCTATGGACTTCCAACTTGGGCAGTTTCTATCCTTCCTCTTCTTGGGACATG
GTGTTCCACATTTGCCCCCTGGCAGAAAAACTCTTGGTCCTTGCCGTTTTCCACCTCCTTCTCAAGTCGTGCAGATATAT
GGCCGTAAAGTGGGTTTGGCCCTAGATCTTCCCCCTCCTAGGTGAAATGAAGACATATTACATAGTCCTGAAATTGCCCA
GTGAGGTCGTGATGATGATGTTTTTAGCACCAGTGAAGATGATGGCTATCCTGAGGACATGGATCAAGATAAGCATGATG
GCAGTACTGATGACAGTGACACCGACGGATCGGATTGAGAAAGTGTGCACCGTGATGATGGTGAGAGAGACAACAATGAA
GAAAAGAAGACAGGTCTGAGTGTATGGTTTGCAGATATACCTGGAAAATCGAAGGAAAAGAAGAACATGAGGGAACTGAC
TCCTCTTCAAGCCACGATGCTTCGTATGGCAGGTCAAGAAATCCCAGAGGAGGGACGGGAAGCAGAGGAATTTTCAGAGG
ACGGTGATGAAGATGATTCTGTTGACTCTGAAGCAGAAAAGGAACCATAAAAACAGCGATTCCATAAAGAGGAATCGCAT
TCTGATGGCACATCCACTGCTTCTTCACAGCAGCAGACTCCCCCTCAGTCTGTTCCTCCTTCTCAGATACAAGCACTACC
CATGCCAGGACCACTACCTCTTGGATCACCACCTGCTTCACCATTATGGCCTCTTAGGCCACCTATGGACCTTCCTCCTG
GACCGCCTCCAGGAGCTCCTCCT

Alignment

ORF - retro_mmul_1329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.56 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKLRETFERILRLYEKENPDIYKELRKLEVEYEQKRAQLSQYFDAVKNAQHVEVESIPLPDMPHAPSNIL
          K.LRETFE.ILRLY.KENPDI.KELRKLE..YEQKRAQL.QY.DAV..AQHVEVESIPLPDMP.APSNI.
Retrocopy K*LRETFEHILRLYDKENPDI*KELRKLEIDYEQKRAQLNQYLDAVEHAQHVEVESIPLPDMPQAPSNIW

Parental  IQDIPLPGAQPPSILKKTSAYGPPTRAVSILPL-LGHGVPRLPPGRKPPGPPPGPPPPQVVQMYGRKVGF
          IQDIPLPG.Q.PSILKK.SAYG.PT.AVSILPL.LGHGVP.LPPGRK..GP...PPP.QVVQ.YGRKVG.
Retrocopy IQDIPLPGVQSPSILKKPSAYGLPTWAVSILPL>LGHGVPHLPPGRKTLGPCRFPPPSQVVQIYGRKVGL

Parental  ALDLPPRRRDEDMLYSPELAQRGHDDDISSTSEDDGYPEDMDQDKHDDSTDDSDTDKSDGESDGDEFVHR
          ALDLPP.R..ED.L.SPE.AQ.G.DDD..STSEDDGYPEDMDQDKHD.STDDSDTD.SD.ES.......R
Retrocopy ALDLPPPR*NEDILHSPEIAQ*GRDDDVFSTSEDDGYPEDMDQDKHDGSTDDSDTDGSD*ESVHRDDGER

Parental  DDGERDNNEEKKSGLSVRFADMPGKSRKKKKNMKELTPLQAMMLRMAGQEIPEEGREVEEFSEDDDEDDS
          D.....N.E.K..GLSV.FAD.PGKS.K.KKNM.ELTPLQA.MLRMAGQEIPEEGRE.EEFSED.DEDDS
Retrocopy D----NNEEKK-TGLSVWFADIPGKS-KEKKNMRELTPLQATMLRMAGQEIPEEGREAEEFSEDGDEDDS

Parental  DDSEAEKQSQKQ--HKEESHSDGASTASSQQQAPPQSVPPSQIQAPPMPGPPPLGPPPAPPLRPPGPPTG
          .DSEAEK...KQ..HKEESHSDG.STASSQQQ.PPQSVPPSQIQA.PMPGP.PLG.PPA.PL.P..PP..
Retrocopy VDSEAEKEP*KQRFHKEESHSDGTSTASSQQQTPPQSVPPSQIQALPMPGPLPLGSPPASPLWPLRPPMD

Parental  LPPGPPPGAPP
          LPPGPPPGAPP
Retrocopy LPPGPPPGAPP

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	89.64 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	66.48 RPM
SRP007412_cerebellum	0.00 RPM	62.38 RPM
SRP007412_heart	0.00 RPM	48.82 RPM
SRP007412_kidney	0.00 RPM	53.17 RPM
SRP007412_liver	0.00 RPM	23.28 RPM
SRP007412_testis	0.19 RPM	519.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1329 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1329 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1329 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1878
Pan troglodytes	retro_ptro_1260
Gorilla gorilla	retro_ggor_1375
Pongo abelii	retro_pabe_1558

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014759	1 retrocopy	retro_btau_20,
Canis familiaris	ENSCAFG00000012926	2 retrocopies	retro_cfam_1369, retro_cfam_1911,
Callithrix jacchus	ENSCJAG00000021611	1 retrocopy	retro_cjac_1737,
Homo sapiens	ENSG00000084463	2 retrocopies	retro_hsap_1878, retro_hsap_4719,
Gorilla gorilla	ENSGGOG00000004448	3 retrocopies	retro_ggor_1375, retro_ggor_1711, retro_ggor_2932,
Macropus eugenii	ENSMEUG00000013971	1 retrocopy	retro_meug_1952,
Myotis lucifugus	ENSMLUG00000015216	1 retrocopy	retro_mluc_1074,
Macaca mulatta	ENSMMUG00000019299	1 retrocopy	retro_mmul_1329 ,
Monodelphis domestica	ENSMODG00000017949	1 retrocopy	retro_mdom_143,
Mustela putorius furo	ENSMPUG00000011619	1 retrocopy	retro_mputfur_280,
Mus musculus	ENSMUSG00000030216	1 retrocopy	retro_mmus_2740,
Nomascus leucogenys	ENSNLEG00000003926	1 retrocopy	retro_nleu_2651,
Oryctolagus cuniculus	ENSOCUG00000017177	1 retrocopy	retro_ocun_974,
Otolemur garnettii	ENSOGAG00000010518	1 retrocopy	retro_ogar_207,
Ochotona princeps	ENSOPRG00000015008	3 retrocopies	retro_opri_107, retro_opri_1159, retro_opri_678,
Pongo abelii	ENSPPYG00000004323	3 retrocopies	retro_pabe_1558, retro_pabe_2099, retro_pabe_3663,
Pan troglodytes	ENSPTRG00000004724	3 retrocopies	retro_ptro_1260, retro_ptro_1637, retro_ptro_3136,
Rattus norvegicus	ENSRNOG00000005505	3 retrocopies	retro_rnor_1287, retro_rnor_2726, retro_rnor_741,
Rattus norvegicus	ENSRNOG00000049593	1 retrocopy	retro_rnor_740,
Sorex araneus	ENSSARG00000007085	1 retrocopy	retro_sara_753,
Sarcophilus harrisii	ENSSHAG00000016649	1 retrocopy	retro_shar_81,
Tupaia belangeri	ENSTBEG00000003394	1 retrocopy	retro_tbel_2213,