RetrogeneDB ID: retro_mmul_2259

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:123938007..123938597(-)
• Located in intron of: ENSMMUG00000001642

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRM
• Ensembl ID: ENSMMUG00000019321
• Aliases: None
• Description: spermidine synthase [Source:RefSeq peptide;Acc:NP_001244736]

Sequence

>retro_mmul_2259
ATGGATCCCAGCCCCAATGGCCCCGCCAGCCTCTGGCCTCACTGCCATTTATAGGACTGATTCTGCAAGACATGCGGTCT
GTGGCCCACCCACGCCTTGTCACTGCAGGTGAAGAAGCTGCCCCACCACCAGTGCTCACAGTACTAGGATACCTTTGTCA
TCTGCACTAAGACCTATGGCAATGTGATGGTGCTGGATGGCATCATCCAGTATAAAGAGAGGAACAAGTTCTCCTACCAG
GAGATTATAGTCAACCTGCCCCTCTGCAGCCACCCCAACACACAAAAGGTGGTGATTATTGAGGACAGGGACAGGAGCAT
TCTGTGCAAGGTGATGTAGCACCCCTCTGTGAAGTCTATGGTCCAGTGTGAGACTGATGAGGATGTCATCCAAGTCTCTC
AGAAGTTCCTGCCAGGCAAAGCTGTTGACTACTTTTGCTCAAAGCTGACCTTACATATGGGTGACGGGTTTGAATTCATG
AAACAGAATTAGGATGCCTTCAGTGTTATCAATGACTCCTCAGATCCCACTGCCTTGCTAAAAGCCTCTTCAAGGAATCC
TACTACCAGCTCATGGAGACAGTCCTCAGG

Alignment

ORF - retro_mmul_2259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.32 %
• Parental protein coverage: 65.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEPGPDGPAASGPAAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLVLDGVIQ
          M.P.P.GPA...P.......F..TC.LWP..ALSLQV..L.HH..S.Y.D..V...KTYGNV.VLDG.IQ
Retrocopy MDPSPNGPASLWPHCHL*D*FCKTCGLWPTHALSLQVKKLPHHQCSQY*DTFVICTKTYGNVMVLDGIIQ

Parental  CTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDEDVIQVSKKFLPGM
          ..ER..FSYQE.I.NLPLCSHPN..KV.II...D...L..V..HPSV.S.VQCE.DEDVIQVS.KFLPG.
Retrocopy YKERNKFSYQEIIVNLPLCSHPNTQKVVIIEDRDRSILCKVM*HPSVKSMVQCETDEDVIQVSQKFLPGK

Parental  AIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMG-PAESLFKESYYQLMKTALK
          A..Y..SKLTLH.GDGFEFMKQN.DAF.V.I.DSSDP....A.SLFKESYYQLM.T.L.
Retrocopy AVDYFCSKLTLHMGDGFEFMKQN*DAFSV-INDSSDPTA<LAKSLFKESYYQLMETVLR

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	14.79 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	51.80 RPM
SRP007412_cerebellum	0.00 RPM	9.62 RPM
SRP007412_heart	0.18 RPM	12.37 RPM
SRP007412_kidney	0.12 RPM	11.15 RPM
SRP007412_liver	0.04 RPM	43.46 RPM
SRP007412_testis	0.04 RPM	7.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2259 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2259 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2259 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1426
Pan troglodytes	retro_ptro_975

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002354	4 retrocopies	retro_cjac_2131, retro_cjac_2524, retro_cjac_3331, retro_cjac_4025,
Dasypus novemcinctus	ENSDNOG00000013348	1 retrocopy	retro_dnov_338,
Homo sapiens	ENSG00000116649	2 retrocopies	retro_hsap_1426, retro_hsap_2313,
Gorilla gorilla	ENSGGOG00000014385	1 retrocopy	retro_ggor_1756,
Loxodonta africana	ENSLAFG00000028297	2 retrocopies	retro_lafr_1175, retro_lafr_894,
Macropus eugenii	ENSMEUG00000007002	2 retrocopies	retro_meug_1330, retro_meug_887,
Myotis lucifugus	ENSMLUG00000017585	1 retrocopy	retro_mluc_2458,
Macaca mulatta	ENSMMUG00000019321	2 retrocopies	retro_mmul_1500, retro_mmul_2259 ,
Mustela putorius furo	ENSMPUG00000016435	1 retrocopy	retro_mputfur_1085,
Mus musculus	ENSMUSG00000006442	1 retrocopy	retro_mmus_3271,
Nomascus leucogenys	ENSNLEG00000009532	3 retrocopies	retro_nleu_1842, retro_nleu_2082, retro_nleu_2778,
Ochotona princeps	ENSOPRG00000012079	1 retrocopy	retro_opri_1119,
Pongo abelii	ENSPPYG00000001892	3 retrocopies	retro_pabe_1181, retro_pabe_1828, retro_pabe_2044,
Pan troglodytes	ENSPTRG00000000138	3 retrocopies	retro_ptro_1403, retro_ptro_1688, retro_ptro_975,
Sus scrofa	ENSSSCG00000027689	1 retrocopy	retro_sscr_1208,