RetrogeneDB ID: retro_mmul_1940

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:32977795..32978364(-)
• Located in intron of: ENSMMUG00000000237

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.4214
• Ensembl ID: ENSMMUG00000012473
• Aliases: None
• Description: proteasome activator complex subunit 2 [Source:RefSeq peptide;Acc:NP_001244558]

Sequence

>retro_mmul_1940
GCCAAGCCTTGTGGTGGGTGCCTGAGCAGGGAGGCCCGCACCCAGGTACCTGTCTTCAGGCAAGAGCTTTCCCAAGAAGG
CAAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATATACCCGCATCAGGCCTTGCAAAACGATTCTCTCATTGTAG
CTGCTTGACCTCCCTCCAGGCCCCACTGGACATCTCCATCCCAGAACCCCCACCCAAGGATGAGGTAGAAACAGAGAAGC
AGGAGAAGAAAGAAGTCCCTGAGTGTGGATTTCTCCCTGGGAATGAGAAGGTTGTCGCTGCTTGCCATGGTTACGCCAGA
AGTCTGGATTCTCAAAGAGAAATGCATGCTGATGATCACATGGATCCAGCACCTGATCCCCAAGACTGAGGATGGAAATG
ATTTGGGGTAGTAATCCAGGAGATGGTGCTGGAGAGGGTGAATGCCGTCAAGACCAAAGTGGAAGCCTTCCAGACAACCA
TTTCCAAATACTTCTCAGAACATGGGGATGCTGTGGCCAAGGCCTCCAAGGAGACCCATGTAACGGTTTACCGGGAGTTG
GTGCAAAAG

Alignment

ORF - retro_mmul_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 80.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVAD-LTSLRAPLDIPIPD
          AKPCG..LS.EAR.QV.VFRQ.L.QE..EFLYRFLPQKIIY..Q.LQ.DSL.VA..LTSL.APLDI.IP.
Retrocopy AKPCGGCLSREARTQVPVFRQELSQEGKEFLYRFLPQKIIYPHQALQNDSLIVAA<LTSLQAPLDISIPE

Parental  PPPKDDEMETDKQE-KKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGND-F
          PPPKD.E.ET.KQE..K......F..G....LSLLA.V.PEVW.LKEKC.L.ITWIQHLIPK.EDGND.F
Retrocopy PPPKD-EVETEKQE>RKKSLSVDFSLGMRR-LSLLAMVTPEVWILKEKCMLMITWIQHLIPKTEDGND<F

Parental  GVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHE
          GV.IQE.VLERVNAVKTKVEAFQTTISKYFSE.GDAVAKASKETHV..YR.LV..
Retrocopy GVVIQEMVLERVNAVKTKVEAFQTTISKYFSEHGDAVAKASKETHVTVYRELVQK

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	8.40 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.17 RPM
SRP007412_cerebellum	0.00 RPM	12.27 RPM
SRP007412_heart	0.00 RPM	17.61 RPM
SRP007412_kidney	0.00 RPM	30.40 RPM
SRP007412_liver	0.00 RPM	35.94 RPM
SRP007412_testis	0.00 RPM	8.56 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1940 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1940 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3033
Pan troglodytes	retro_ptro_2046
Gorilla gorilla	retro_ggor_2093
Pongo abelii	retro_pabe_2512

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940 , retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,