RetrogeneDB ID: retro_mmul_2101

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:106193371..106193880(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSMMUG00000015466
• Aliases: None
• Description: None

Sequence

>retro_mmul_2101
AGGCGAGAACCACTGTCTCTGAACAACCTAAGGAAGAGGAACGTGGAATCTGGAGAAGAGCTGGCGTCCAGGCTGGACCA
CTGCAGAGCCAAGACCACAGCGTACATCCTCCTCATCACACGTTGCCAATACCATGTGGACGGCTCCCTGGAAAAGGACT
GCGGTCTGAACCTGCTGGGTCGTGAACCGGTAGAACTAACTGGACTCCAATTTGCAAGCCTGGGGTTGAGGTTTAATAAA
ATCGTCCATTCCTCCATGACCCACCCCATAGAAACCACTGGCTTCAGCAACAGGCACCTGCCAAACGTCTGCAAAGTCCA
CACAGACCTGGGGCGGGAAGCCCCCTCGTCAAGCCAGCCTGGCAGCGTATCACTGGAAGCGGCCACTGGGCATGTTGTGA
AGATGGGAGTGCGGATCGAGGCAGCGCTCCGAAACTGCATCCCTCGGGGGATGCCAAGCAGGGGGACGATAATTAGGAGA
TCTTCCGATGTCACGCCAATGTCATTCGT

Alignment

ORF - retro_mmul_2101 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 97.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RREPLSLINLRKRNVESGEEELASKLDHYKAKATRHIFLIRHSQYHVDGSLEKDRTLTPLGREQAELTGL
          RREPLSL.NLRKRNVESGEE.LAS.LDH..AK.T..I.LI...QYHVDGSLEKD..L..LGRE..ELTGL
Retrocopy RREPLSLNNLRKRNVESGEE-LASRLDHCRAKTTAYILLITRCQYHVDGSLEKDCGLNLLGREPVELTGL

Parental  RLASLGLKFNKIVHSSMTRAIETTDIISRHLPGVCKVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGAR
          ..ASLGL.FNKIVHSSMT..IETT....RHLP.VCKV.TDL.RE.AP....P...............G.R
Retrocopy QFASLGLRFNKIVHSSMTHPIETTGFSNRHLPNVCKVHTDLGRE-APSSSQPGSVSLEAATGHVVKMGVR

Parental  IEAAFRNYIHRA-DARQEEDSYEIFICHANVIR
          IEAA.RN.I.R..DA.Q..D..EIF.CHANVIR
Retrocopy IEAALRNCIPRG<DAKQGDDN*EIFRCHANVIR

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	6.61 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	17.45 RPM
SRP007412_cerebellum	0.00 RPM	4.71 RPM
SRP007412_heart	0.00 RPM	5.54 RPM
SRP007412_kidney	0.00 RPM	10.21 RPM
SRP007412_liver	0.00 RPM	13.38 RPM
SRP007412_testis	6.37 RPM	6.90 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2101 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2101 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3363
Pan troglodytes	retro_ptro_2286

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101 ,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,