RetrogeneDB ID: retro_mmul_782

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:7067439..7067892(+)
• Located in intron of: ENSMMUG00000001781

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2966
• Ensembl ID: ENSMMUG00000013786
• Aliases: None
• Description: destrin (actin depolymerizing factor) [Source:RefSeq peptide;Acc:NP_001182421]

Sequence

>retro_mmul_782
GCCTCAGGAGTGCAAGTTGCTGATGAAGTATGTCGCATTTTTTATGACATGAGACTTTGTAAATGCTCAACACCAGAAGA
AATCAAGAAAAGAAAGAAGACTGTCATTTTTTTGTCTCAGTGCAGACAAAAAATGCATCATTGTAGAAGGCAAAGAGATC
TTGGTTGGAGATGTTGGTGTAACCATAACTGAGCCTTTCAAGCATTTTGTTGGAATGCTTCCTGAAAAAGATTGTCCCTA
TGCTTTGTACGATGCAAGCTTTGAAACAAAATAATCCAGAAGAATTGATGTTTTTTTGTGGGCACCAGAACTAGCACCTC
TGAAAAGTAAAATGATCTATGCAACTCCAAGGATGCAATTAAAAAGAAATTTCAAGGCATAAAACATGAATGTCAAGCAA
ATGGACCAGAAGATCTCAGTCGGGCTTGTATTGCTGAAAAGTTGGGTGGATCC

Alignment

ORF - retro_mmul_782 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 93.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASGVQVADEVCRIFYDMKVRKCSTPEEIKKRKKAVIF-CLSADKKCIIVEEGKEILVGDVGVTITDPFKH
          ASGVQVADEVCRIFYDM...KCSTPEEIKKRKK.VIF.CLSADKKCIIV.EGKEILVGDVGVTIT.PFKH
Retrocopy ASGVQVADEVCRIFYDMRLCKCSTPEEIKKRKKTVIF>CLSADKKCIIV-EGKEILVGDVGVTITEPFKH

Parental  FVGMLPEKDCRYALYDASFETKESRKEELMFFLWAPELAPLKSKMIYA-SSKDAIKKKFQGIKHECQANG
          FVGMLPEKDC.YALYDASFETK.SR......FLWAPELAPLKSKMIYA..SKDAIKKKFQGIKHECQANG
Retrocopy FVGMLPEKDCPYALYDASFETK*SRRIDV--FLWAPELAPLKSKMIYA<NSKDAIKKKFQGIKHECQANG

Parental  PEDLNRACIAEKLGGS
          PEDL.RACIAEKLGGS
Retrocopy PEDLSRACIAEKLGGS

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	148.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	103.92 RPM
SRP007412_cerebellum	0.06 RPM	122.95 RPM
SRP007412_heart	0.00 RPM	160.70 RPM
SRP007412_kidney	0.00 RPM	134.97 RPM
SRP007412_liver	0.00 RPM	46.27 RPM
SRP007412_testis	0.08 RPM	21.49 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_782 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_782 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_782 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_952
Pan troglodytes	retro_ptro_659
Pongo abelii	retro_pabe_812

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015434	1 retrocopy	retro_btau_880,
Choloepus hoffmanni	ENSCHOG00000003110	5 retrocopies	retro_chof_1308, retro_chof_1656, retro_chof_1758, retro_chof_2297, retro_chof_72,
Cavia porcellus	ENSCPOG00000005573	2 retrocopies	retro_cpor_700, retro_cpor_812,
Dasypus novemcinctus	ENSDNOG00000000934	1 retrocopy	retro_dnov_24,
Erinaceus europaeus	ENSEEUG00000011893	1 retrocopy	retro_eeur_529,
Homo sapiens	ENSG00000125868	1 retrocopy	retro_hsap_952,
Gorilla gorilla	ENSGGOG00000009007	1 retrocopy	retro_ggor_768,
Microcebus murinus	ENSMICG00000013687	1 retrocopy	retro_mmur_765,
Macaca mulatta	ENSMMUG00000013786	1 retrocopy	retro_mmul_782 ,
Macaca mulatta	ENSMMUG00000019016	5 retrocopies	retro_mmul_316, retro_mmul_493, retro_mmul_556, retro_mmul_667, retro_mmul_705,
Mus musculus	ENSMUSG00000015932	1 retrocopy	retro_mmus_3314,
Nomascus leucogenys	ENSNLEG00000009679	1 retrocopy	retro_nleu_2458,
Oryctolagus cuniculus	ENSOCUG00000027456	1 retrocopy	retro_ocun_1891,
Ochotona princeps	ENSOPRG00000000976	2 retrocopies	retro_opri_1078, retro_opri_696,
Pongo abelii	ENSPPYG00000010727	1 retrocopy	retro_pabe_812,
Pan troglodytes	ENSPTRG00000013275	1 retrocopy	retro_ptro_659,
Pteropus vampyrus	ENSPVAG00000000420	1 retrocopy	retro_pvam_1275,
Rattus norvegicus	ENSRNOG00000005924	1 retrocopy	retro_rnor_1710,
Sus scrofa	ENSSSCG00000007085	1 retrocopy	retro_sscr_954,
Tupaia belangeri	ENSTBEG00000017634	8 retrocopies	retro_tbel_1206, retro_tbel_1977, retro_tbel_2425, retro_tbel_2880, retro_tbel_2881, retro_tbel_4020, retro_tbel_679, retro_tbel_851,
Tursiops truncatus	ENSTTRG00000007291	1 retrocopy	retro_ttru_1503,