RetrogeneDB ID: retro_mmul_2590

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:64998362..64999022(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTFR1
• Ensembl ID: ENSMMUG00000011263
• Aliases: None
• Description: None

Sequence

>retro_mmul_2590
CATGCAACAGAATCGGGTCCCAACCACCCAGGAGAGGAGGCAGTGGTGTCTTTTGTGGCTGTTGAATGGGTAGCCAAAGG
AGAGTGTTCAACAAGACCAAGAACAGAAGCCAGGTCAAGGCCATCCTTTCACGATGACCTTTTCTTTAAGGAGGCCCCAA
GCAGACAGATTTCCTTACCAGACTTGTCTCAAGAAGAGCCTCAGCTGAAAACCCCAGCCTGGTAAATGAGGAGGCACTGC
AGAAGATTTGTGCTCTTGAAAATGAACTTGCTGCTCTCAGAGCCCAGATTACCAAAATTGTGACTCAGCAATAGCAGGAA
AATCTCATTGAAAGTGACTTAGATTTTACCACATCTGTTACCACACCACCATCCCCTCCACCTCTCCTGCCACTCTAGCT
CCCCTCTCCACTGGGACTCCACCAAAGTATATTTGATACTGATCTGATTAGAGGGTGAGGATGGAAAAAAGCCAATGCTG
GAAAGACGTTGGCTAAGAACAATCCAAAAAAAAGCTGACATGGCAAAAAAGTTAGGGATTCTTAAAGATATGATCAGTGT
AGAACTTTAGTCAGTAAAAACGTCAGAGCAAGATGTATAGCCCAAGTCAGTGGATGCTGCTGGCCCTGGTCCCGTCATAG
CAGACGCTCTGAAAAAGAAA

Alignment

ORF - retro_mmul_2590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 71.7 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HATEWSPSHPGEDAVASFADVGWVAKEEGECSARLRTEVRSRPPLQDDLLFFEKAPSRQISLPDLSQEEP
          HATE..P.HPGE.AV.SF..V.WVAK..GECS.R.RTE.RSRP...DDL.FF..APSRQISLPDLSQEEP
Retrocopy HATESGPNHPGEEAVVSFVAVEWVAK--GECSTRPRTEARSRPSFHDDL-FFKEAPSRQISLPDLSQEEP

Parental  QLKTPA-LANEEALQKICALENELAALRAQIAKIVTQQEQQNLIAGDLDSTTSGTTLPPPPPPPPPPPPP
          QLKTPA.L.NEEALQKICALENELAALRAQI.KIVTQQ.Q.NLI..DLD.TTS.TT.P.PPP..P...P.
Retrocopy QLKTPA<LVNEEALQKICALENELAALRAQITKIVTQQ*QENLIESDLDFTTSVTTPPSPPPLLPL*LPS

Parental  PLGLHQSVSAIDLIKERREKRANAGKTLVKNN-PKKPEMPNMLEILKDMNSVKLRSVKRSEQDVKPKPVD
          PLGLHQS....DLI.....K.ANAGKTL.KNN......M...L.ILKDM.SV.L.SVK.SEQDV.PK.VD
Retrocopy PLGLHQSIFDTDLIRG*GWKKANAGKTLAKNN>XXXADMAKKLGILKDMISVEL*SVKTSEQDV*PKSVD

Parental  ATDPAALIAEALKRK
          A..P...IA.ALK.K
Retrocopy AAGPGPVIADALKKK

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	3.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	1.51 RPM
SRP007412_cerebellum	0.00 RPM	8.46 RPM
SRP007412_heart	0.00 RPM	6.24 RPM
SRP007412_kidney	0.00 RPM	26.17 RPM
SRP007412_liver	0.00 RPM	13.10 RPM
SRP007412_testis	0.00 RPM	130.95 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2590 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2590 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2590 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4849
Pongo abelii	retro_pabe_3769

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012281	1 retrocopy	retro_amel_1640,
Choloepus hoffmanni	ENSCHOG00000006664	3 retrocopies	retro_chof_1268, retro_chof_2700, retro_chof_483,
Dipodomys ordii	ENSDORG00000016322	1 retrocopy	retro_dord_293,
Homo sapiens	ENSG00000066855	1 retrocopy	retro_hsap_4849,
Macaca mulatta	ENSMMUG00000011263	1 retrocopy	retro_mmul_2590 ,
Mustela putorius furo	ENSMPUG00000009909	2 retrocopies	retro_mputfur_1244, retro_mputfur_894,
Oryctolagus cuniculus	ENSOCUG00000008165	1 retrocopy	retro_ocun_1594,
Pongo abelii	ENSPPYG00000018631	1 retrocopy	retro_pabe_3769,
Rattus norvegicus	ENSRNOG00000021359	1 retrocopy	retro_rnor_1821,
Tarsius syrichta	ENSTSYG00000010102	1 retrocopy	retro_tsyr_1899,