RetrogeneDB ID: retro_mmul_102

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:35777666..35778425(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000030357
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MMU.3696
• Ensembl ID: ENSMMUG00000017461
• Aliases: None
• Description: partner of NOB1 [Source:RefSeq peptide;Acc:NP_001165579]

Sequence

>retro_mmul_102
ATGGAATCCGAAATGGAAGCGCAGAGCGCCGGGGCAGAGGAGGGCTTTACCCAGGTCACCGGTAAGGGTGGCCGGCGGGC
GAAGAAACGACAGGCTGAACAGCTGTCCGCAGCGGGAGAGGGCGGGGATGCGGGCCGGATGGACACAGAGGAGGCCAGGC
CGGCGAAGAGGCCCGTCTTCCCACCCCTCTGTGGGGACGGGCTCCTGAGTGGAAAAGAAGGAACAAGGAAAATTCCAGTC
CCAGCTAACAGATACACACCATTGAAAGAAAACTGGATGAAGATATTTACTCCTATTGTGGAACATTTGGGACTTCAGAT
ACGCTTTAACTTGAAATCAAGGAATGTAGAAATCAGGACTTGTAAAGAAACCAAGGATGTTAGTGCTCTGACAAAAGCAG
CTGATTTTGTGAAAGCTTTTATTCTAGGCTTTCAGGTGGAGGATGCACTTGCCCTCATCAGGTTGGATGACCTCTTCCTA
GAGTCTCTTGAAATTACAGATGTTAAACCCCTAAAGGGAGACCATCTATCCAGGGCAATAGGAAGAATCGCTGGCAAAGG
AGGAAAAACCAAATTCACCATAGAGAATGTGACACGGACGCGGATAGTTTTGGCTGATGTGAAAGTTCACATCCTTGGCT
CCTTCCAAAACATCAAGATGGCAAGAACTGCCATTTGCAACCTAATCTTGGGAAATCTTCCTTCCAAGGTTTATGGCAAT
ATTCGAGCTGTGGCTAGCAGATCAGCAGATGGATTCTGA

Alignment

ORF - retro_mmul_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESEMEAQSAGAEEGFTQVTRKGGRRAKKRQAEQLSAAGEGGDAGRMDTEEARPAKRPVFPPLCGDGLLS
          MESEMEAQSAGAEEGFTQVT.KGGRRAKKRQAEQLSAAGEGGDAGRMDTEEARPAKRPVFPPLCGDGLLS
Retrocopy MESEMEAQSAGAEEGFTQVTGKGGRRAKKRQAEQLSAAGEGGDAGRMDTEEARPAKRPVFPPLCGDGLLS

Parental  GKEETRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF
          GKE.TRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF
Retrocopy GKEGTRKIPVPANRYTPLKENWMKIFTPIVEHLGLQIRFNLKSRNVEIRTCKETKDVSALTKAADFVKAF

Parental  ILGFQVEDALALIRLDDLFLESFEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH
          ILGFQVEDALALIRLDDLFLES.EITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH
Retrocopy ILGFQVEDALALIRLDDLFLESLEITDVKPLKGDHLSRAIGRIAGKGGKTKFTIENVTRTRIVLADVKVH

Parental  ILGSFQNIKMARTAICNLILGNPPSKVYGNIRAVASRSADRF
          ILGSFQNIKMARTAICNLILGN.PSKVYGNIRAVASRSAD.F
Retrocopy ILGSFQNIKMARTAICNLILGNLPSKVYGNIRAVASRSADGF

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	0.11 RPM	6.72 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	7.06 RPM
SRP007412_cerebellum	0.00 RPM	7.62 RPM
SRP007412_heart	0.00 RPM	5.95 RPM
SRP007412_kidney	0.00 RPM	8.92 RPM
SRP007412_liver	0.00 RPM	4.59 RPM
SRP007412_testis	0.11 RPM	5.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_102 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003256	1 retrocopy	retro_cfam_1886,
Callithrix jacchus	ENSCJAG00000006564	3 retrocopies	retro_cjac_2615, retro_cjac_273, retro_cjac_4127,
Felis catus	ENSFCAG00000025330	2 retrocopies	retro_fcat_1521, retro_fcat_864,
Loxodonta africana	ENSLAFG00000000046	1 retrocopy	retro_lafr_419,
Microcebus murinus	ENSMICG00000010897	1 retrocopy	retro_mmur_516,
Myotis lucifugus	ENSMLUG00000010850	1 retrocopy	retro_mluc_1719,
Macaca mulatta	ENSMMUG00000017461	2 retrocopies	retro_mmul_102 , retro_mmul_352,
Nomascus leucogenys	ENSNLEG00000009993	1 retrocopy	retro_nleu_2389,
Oryctolagus cuniculus	ENSOCUG00000006100	1 retrocopy	retro_ocun_47,
Otolemur garnettii	ENSOGAG00000016637	1 retrocopy	retro_ogar_3025,
Pongo abelii	ENSPPYG00000012353	1 retrocopy	retro_pabe_1232,
Rattus norvegicus	ENSRNOG00000005524	1 retrocopy	retro_rnor_712,
Sus scrofa	ENSSSCG00000008352	2 retrocopies	retro_sscr_114, retro_sscr_352,
Tarsius syrichta	ENSTSYG00000004007	1 retrocopy	retro_tsyr_1625,