RetrogeneDB ID: retro_mmul_1261

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:42714183..42714882(-)
• Located in intron of: ENSMMUG00000004184

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.192
• Ensembl ID: ENSMMUG00000008532
• Aliases: None
• Description: None

Sequence

>retro_mmul_1261
CCCCACCTTCCAACCGCGCCAGATCGGCATCCGCTGCCAAAGTCAGTAAAAAGGAGCTCAACTCCAGCCACTACAGGGCT
GACGAGACCTCAGGAAAACAGCAGGAAGCAATTGAACACATTGATGAAATCCAAAATGAAACAAACAGACTTAATGAACA
AGCCAGTGAGGAGATTTTGAAAGCAGAACAGAAATGTAACAAACTCCGCTAACCATTTTTTTCAGAAGAGATCAGAATTG
ATCACCAAAATCCCACATTTGGGGATAACAACATTTATCAACCATCCACAGGTGTCTGCACTGCTTGGGGAGGAGGAAGA
AGCGGCACTGCATTATTTGAGCAGAGTTGAAGTGACAGAATTTGAATATATTTAATCAGATTACGGAATAGATTTTTATT
TTGATCAAAATCCTTACTTTGAAAATAAAGTTCTGTCCAAAGAATTTCATCTGAATGAGAGTGGTGATCCATCTTTAAAG
TCCACTGCAATCAAATGGAAATCTGGAAAGGATTTGACAAAGCGTTCAAGTCAAACGCAGAATAAAGCCGGCAGGAAGAA
GCAGCATGAGGAACCAGGGAGCTTCTTTACCTGGTTTACTGACCATTCTGATGCAGGTGCTGATGAGTTAGGAGAGGTCA
TCAAAGATGATATTTGGCCAAGCCCATTACAGTACTACTTGGTTCCCGATGTGGATGAT

Alignment

ORF - retro_mmul_1261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.6 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLLPQKKKPRPPPA-LGPEETSASAGLPKKGEKEQQEAIEHIDEVQNEIDRLNEQASEEILKVEQKYNKL
          P.LP......P.P......E...S..........QQEAIEHIDE.QNE..RLNEQASEEILK.EQK.NKL
Retrocopy PHLPTAPDRHPLPK<VSKKELNSSHYRADETSGKQQEAIEHIDEIQNETNRLNEQASEEILKAEQKCNKL

Parental  RQPFF-QKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENP
          R.PFF.QKRSELI.KIP....TTF.NHPQVSALLGEE.E.ALHYL.RVEVTEFE.I.S.Y.IDFYFD.NP
Retrocopy R*PFF>QKRSELITKIPHLGITTFINHPQVSALLGEEEEAALHYLSRVEVTEFEYI*SDYGIDFYFDQNP

Parental  YFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGAD
          YFENKVLSKEFHLNESGDPS.KST.IKWKSGKDLTKRSSQTQNKA.RK.QHEEP.SFFTWFTDHSDAGAD
Retrocopy YFENKVLSKEFHLNESGDPSLKSTAIKWKSGKDLTKRSSQTQNKAGRKKQHEEPGSFFTWFTDHSDAGAD

Parental  ELGEVIKDDIWPNPLQYYLVPDMDD
          ELGEVIKDDIWP.PLQYYLVPD.DD
Retrocopy ELGEVIKDDIWPSPLQYYLVPDVDD

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	0.45 RPM	51.10 RPM
SRP007412_brain_prefrontal_cortex	0.48 RPM	47.36 RPM
SRP007412_cerebellum	3.29 RPM	49.21 RPM
SRP007412_heart	0.12 RPM	40.04 RPM
SRP007412_kidney	0.12 RPM	39.20 RPM
SRP007412_liver	0.04 RPM	11.68 RPM
SRP007412_testis	0.90 RPM	20.69 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1261 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1261 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1847
Pan troglodytes	retro_ptro_1232
Pongo abelii	retro_pabe_1452

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Dasypus novemcinctus	ENSDNOG00000002802	3 retrocopies	retro_dnov_160, retro_dnov_1830, retro_dnov_464,
Erinaceus europaeus	ENSEEUG00000006238	11 retrocopies	retro_eeur_152, retro_eeur_166, retro_eeur_173, retro_eeur_210, retro_eeur_260, retro_eeur_287, retro_eeur_452, retro_eeur_659, retro_eeur_696, retro_eeur_700, retro_eeur_701,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Homo sapiens	ENSG00000119335	14 retrocopies	retro_hsap_1336, retro_hsap_1389, retro_hsap_1847, retro_hsap_241, retro_hsap_269, retro_hsap_2719, retro_hsap_2721, retro_hsap_3075, retro_hsap_3088, retro_hsap_3326, retro_hsap_3358, retro_hsap_420, retro_hsap_4722, retro_hsap_806,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta	ENSMMUG00000008532	11 retrocopies	retro_mmul_1133, retro_mmul_1261 , retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,