RetrogeneDB ID: retro_mmul_1011

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:112365987..112366414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2D
• Ensembl ID: ENSMMUG00000001989
• Aliases: None
• Description: DNA-directed RNA polymerase II subunit RPB4 [Source:RefSeq peptide;Acc:NP_001254716]

Sequence

>retro_mmul_1011
ATGGCAGCAGGCGGCAGCGATCCGCAGGCTGGCAATGTAGAGGAGGACACTTAACAGCTCATGTTTCCTGAAGAGTTTGA
AACAGCGAAGACACTTCTAAATTCAGAAATTCATGTGCTTCTGGAACATCGAAAGCAATAGAACGAGAGTGCAGAGGATG
AACAGGAACTCTCAGAAGTCTTTGTGTAAACAAAGAAACTACACAGGCTGTTTCAGTGGTTTCGAAAACAGAGAGACCAT
TGCCAGTATTTGTAGCTTGTTACTCCAGAAAAAGCTTCATAAATTTAAGTTGGTCTGTTTGGCCAACCTTTGCCCAGAGA
CTGCTGAGGAGTCCAAGGCTCCAATCCCAAGCTTGGAGAGGTGGTTTGAAGATGAGGAGCTGTAGCAGATTCTTGATGGT
AGCCAGACAAAGGGCAGCTTTCAGTAT

Alignment

ORF - retro_mmul_1011 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAGGGDPRAGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFM-KTLNYTA
          MAAGG.DP.AG.VEED..QL.FP.EFETA.TLLNSE.H.LLEHRKQ.NESAEDEQELSEVF..K..NYT.
Retrocopy MAAGGSDPQAGNVEEDT*QLMFPEEFETAKTLLNSEIHVLLEHRKQ*NESAEDEQELSEVFV>KQRNYTG

Parental  RFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRS
          .FS.F.NRETIAS..SLLLQKKLHKF.L.CLANLCPETAEESKA.IPSLE..FEDEEL.QILD..QTK.S
Retrocopy CFSGFENRETIASICSLLLQKKLHKFKLVCLANLCPETAEESKAPIPSLERWFEDEEL*QILDGSQTKGS

Parental  FQY
          FQY
Retrocopy FQY

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	5.38 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.24 RPM
SRP007412_cerebellum	0.00 RPM	3.62 RPM
SRP007412_heart	0.00 RPM	3.24 RPM
SRP007412_kidney	0.00 RPM	4.93 RPM
SRP007412_liver	0.00 RPM	1.54 RPM
SRP007412_testis	0.00 RPM	12.59 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1011 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1011 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1011 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1571
Gorilla gorilla	retro_ggor_1658
Pongo abelii	retro_pabe_1933

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011746	1 retrocopy	retro_amel_1020,
Canis familiaris	ENSCAFG00000004311	2 retrocopies	retro_cfam_1403, retro_cfam_2188,
Choloepus hoffmanni	ENSCHOG00000013850	3 retrocopies	retro_chof_1003, retro_chof_1568, retro_chof_1920,
Dasypus novemcinctus	ENSDNOG00000008527	1 retrocopy	retro_dnov_734,
Felis catus	ENSFCAG00000027816	1 retrocopy	retro_fcat_1148,
Gorilla gorilla	ENSGGOG00000004723	1 retrocopy	retro_ggor_1658,
Macaca mulatta	ENSMMUG00000001989	1 retrocopy	retro_mmul_1011 ,
Monodelphis domestica	ENSMODG00000018653	4 retrocopies	retro_mdom_1320, retro_mdom_457, retro_mdom_689, retro_mdom_851,
Mustela putorius furo	ENSMPUG00000016685	1 retrocopy	retro_mputfur_611,
Mus musculus	ENSMUSG00000024258	1 retrocopy	retro_mmus_1331,
Oryctolagus cuniculus	ENSOCUG00000021449	1 retrocopy	retro_ocun_35,
Ochotona princeps	ENSOPRG00000005327	2 retrocopies	retro_opri_233, retro_opri_725,
Pongo abelii	ENSPPYG00000012759	1 retrocopy	retro_pabe_1933,
Pan troglodytes	ENSPTRG00000012436	1 retrocopy	retro_ptro_1571,
Sorex araneus	ENSSARG00000009037	1 retrocopy	retro_sara_420,
Sarcophilus harrisii	ENSSHAG00000014817	1 retrocopy	retro_shar_728,
Ictidomys tridecemlineatus	ENSSTOG00000023329	3 retrocopies	retro_itri_1323, retro_itri_145, retro_itri_600,