RetrogeneDB ID: retro_mmul_400

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:104942381..104943077(+)
• Located in intron of: ENSMMUG00000006780

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2487
• Ensembl ID: ENSMMUG00000007740
• Aliases: None
• Description: None

Sequence

>retro_mmul_400
CAGTGCTGTCCTAATTGCTGAGGTATTGGAATGCAAATAAGAATTCATCAGATAGAACCCGGAATGGCTCAGCAAATTCA
AGCTGTGTGCATGGAAACCCAGGGCCATGCAGAACAGATCAGTCCTCAAGATAGATGTAAAAGCTGCAATGGAAAGAAGA
TAGTTTTGGGAGAAGACAGTTCTAGTAATTCATATTGATAGAGGCATGAAAGATGGCCAGAAAATAACATCCCATGATGA
AGCAGACCAAAAACCAGGACTGGAGCCAGGAGATATTATCATTGCGTTAGATCAGAAGGACCATGCTGTTTTTGACAAAG
AGAAGACCTTTTCATATATATGGACATACAGCTGGTTGTAGTATTGCATGGCTTCTGAAAGCCAATATCCACTCTTGACA
ACTGAACCATAGTCATCATCTCTCATCCAGATCATGTTGTCAAGCAAGGAGCCATCGAGTATGTGTTAAATGAAGGCAGG
CCAATTTATTGTAGACCACATGAAAAGGTGCTTAATCATTGAATTTTAAGGTAAGCTTTCTTGATAATGGCTTTCCCTTT
TTTGACAAACTTCTTGCTGGAAAAACTCCTACCCAAGAGGAAAGAAGTAGAAGAGACTGATGAGATGAATCAAGTAGAAT
TGGTGGACTTTGATTCAAATCAGGAAAGACGACGCTGATGCCACTACAATGGAGAA

Alignment

ORF - retro_mmul_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.87 %
• Parental protein coverage: 58.44 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVR-EKKILEVHIDKGM
          .CCPNC.G.GMQIRIHQI.PGM.QQIQ.VCME.QGH.E.ISP.DRCKSCNG.KIV..EK..L..HID.GM
Retrocopy QCCPNC*GIGMQIRIHQIEPGMAQQIQAVCMETQGHAEQISPQDRCKSCNGKKIVL>EKTVLVIHIDRGM

Parental  KDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAV-FTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTI
          KDGQKIT.H.E.DQ.PGLEPGDIII.LDQKDHAV.F..R.EDLF..MDIQLV..L.GF.KPISTLDN.TI
Retrocopy KDGQKITSHDEADQKPGLEPGDIIIALDQKDHAV<F*QR-EDLFIYMDIQLVVVLHGF*KPISTLDN*TI

Parental  VITSHPGQIVKHGDIKCVLNEGMPIYRRPYE-KGRLIIEFKVNFPENGFLSPDKL-SLLEKLLPERKE-V
          VI.SHP...VK.G.I..VLNEG.PIY.RP.E.KG.....FKV.F..NGF...DKL.S......P..K..V
Retrocopy VIISHPDHVVKQGAIEYVLNEGRPIYCRPHE<KGA*SLNFKVSFLDNGFPFFDKL<SCWKNSYPRGKK<V

Parental  EETDEMDQVELVDFDPNQERRR--HYNGE
          EETDEM.QVELVDFD.NQERRR..HYNGE
Retrocopy EETDEMNQVELVDFDSNQERRR*CHYNGE

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	212.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	192.85 RPM
SRP007412_cerebellum	0.00 RPM	107.58 RPM
SRP007412_heart	0.00 RPM	79.67 RPM
SRP007412_kidney	0.00 RPM	94.25 RPM
SRP007412_liver	0.00 RPM	82.02 RPM
SRP007412_testis	0.00 RPM	424.47 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_400 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_400 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_177

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Felis catus	ENSFCAG00000008729	5 retrocopies	retro_fcat_1241, retro_fcat_1407, retro_fcat_1502, retro_fcat_1984, retro_fcat_811,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Macaca mulatta	ENSMMUG00000002247	1 retrocopy	retro_mmul_36,
Macaca mulatta	ENSMMUG00000007740	6 retrocopies	retro_mmul_1313, retro_mmul_1802, retro_mmul_2477, retro_mmul_2482, retro_mmul_2625, retro_mmul_400 ,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Nomascus leucogenys	ENSNLEG00000005268	4 retrocopies	retro_nleu_1255, retro_nleu_2550, retro_nleu_2793, retro_nleu_509,
Oryctolagus cuniculus	ENSOCUG00000004833	2 retrocopies	retro_ocun_516, retro_ocun_70,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Sus scrofa	ENSSSCG00000011000	2 retrocopies	retro_sscr_134, retro_sscr_984,