RetrogeneDB ID: retro_mmul_1500

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:21739379..21740135(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000021570
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mmul_1500
GACATCCTAGTCTTCCGCAGTAAGACCTATGGCAACGTGCTAGTGTTGGACGGTGTCATCCAGTGCACGGAGAGGGACGA
GTTCTCCTACCTGGAGATGATGGCCAACCTGCCTCTCTGCAGCCACCCCAACCCGCGAAAGGTGCTGATCATGGGGGGCG
GAGATGGAGGTGTCCTGCATGAGGTGGTGAAGCACCCCTCCCTGGAGTCTGTGGTCCAGTGTGAGATCGACGAGGATGTC
ATCCAAGTCTCCAAGAAGTTCCTGCCAGGCATGGCTATTGGCTACTCTAGCTCGAAGCTGACCCTATATGTGGGTGACGG
TTTTGAGTTCATGAAACAGAATCAGGATGCCTTCGATGTGATCATCACTGACTCCTCAGACCCTATGGGCCCAACCGAAA
GTCTCTTCAAGGAGTCCTATTACCAGCTCGTGAAGACGGCCCTCATGGAAGATGGTGTCCTCTGCTGCCAGGGTGAGTGC
CAGTGGCTGCACCTGGACCTCATGAAGGAGATGCGGCAGTTCTGCCAGTCCCCATTCCCCGTAGTGGCTTATGCCTACTG
CACCATCCCCACCTACCCCAGCAGCCAGATCGGCTTCATGCTGTGCAGCAAGAACTTGAGCACCAACTTCCAGGAGCCGG
TGCAGTCGCTGACGCAGCAGCAGGTGGCACAGATGCAGCTGAAGGACTACAACTCTGACGTGCACCGCACCGCCTTTGTG
CTGCCCGAGTTTGCCCGCAAGGCCCTGAATGATGTG

Alignment

ORF - retro_mmul_1500 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.25 %
• Parental protein coverage: 83.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DILVFRSKTYGNVLVLDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVES
          DILVFRSKTYGNVLVLDGVIQCTERDEFSY.EM.ANLPLCSHPNPRKVLI.GGGDGGVL.EVVKHPS.ES
Retrocopy DILVFRSKTYGNVLVLDGVIQCTERDEFSYLEMMANLPLCSHPNPRKVLIMGGGDGGVLHEVVKHPSLES

Parental  VVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESY
          VVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTL.VGDGFEFMKQNQDAFDVIITDSSDPMGP.ESLFKESY
Retrocopy VVQCEIDEDVIQVSKKFLPGMAIGYSSSKLTLYVGDGFEFMKQNQDAFDVIITDSSDPMGPTESLFKESY

Parental  YQLMKTALKEDGVLCCQGECQWLHLDLIKEMRQFCQSLFPVVAYAYCTIPTYPSGQIGFMLCSKNPSTNF
          YQL.KTAL.EDGVLCCQGECQWLHLDL.KEMRQFCQS.FPVVAYAYCTIPTYPS.QIGFMLCSKN.STNF
Retrocopy YQLVKTALMEDGVLCCQGECQWLHLDLMKEMRQFCQSPFPVVAYAYCTIPTYPSSQIGFMLCSKNLSTNF

Parental  QEPVQPLTQHQVAQMQLKYYNSDVHRAAFVLPEFARKALNDV
          QEPVQ.LTQ.QVAQMQLK.YNSDVHR.AFVLPEFARKALNDV
Retrocopy QEPVQSLTQQQVAQMQLKDYNSDVHRTAFVLPEFARKALNDV

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	0.16 RPM	51.80 RPM
SRP007412_cerebellum	0.06 RPM	9.62 RPM
SRP007412_heart	0.06 RPM	12.37 RPM
SRP007412_kidney	0.12 RPM	11.15 RPM
SRP007412_liver	0.08 RPM	43.46 RPM
SRP007412_testis	0.11 RPM	7.58 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1500 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1500 has 0 orthologous retrocopies within eutheria group .

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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,