RetrogeneDB ID: retro_mmul_2362

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:101855122..101855865(-)
• Located in intron of: ENSMMUG00000022186

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSMMUG00000002689
• Aliases: None
• Description: None

Sequence

>retro_mmul_2362
CCATCAGTTATAATCTATCCATGAGAATAAGCTCGGTATAAAAAGGTGACTTCATCTAAGTGCTTTCTTTCAATTAAGGA
AAGCATCACAGACAATAAAAGGAACCAGGGGGAGCTCTCTCCCAGCCCACCTTTGTTGAATCCATCCACACCACAGTCCA
CAGAGAGTCAGACAACCACAGCTGAACCAGCCACCCACAAAAGGCACAAAGCCAAGCCGGAAGCATTGCCGGCTGTGAGG
CGGTCCACATGCCACATCACCAACTGCAACAGGCTGGCTGAGAGCAGGCGTCACCTCACCCAGGTGCCAGCAGCAGGCCA
CATCGACCAGCATGCTCCAGGCTGCTCCTGAACCTGGAGAAGAAAACACCTGTGCATCATCTTCAACCTCTGCCTCCTAG
CAAGGAAGAAAGTGCTGCATTTACTGGTTTTGAAGGGAAAAGAACTAACTAAATAAATGAAGTCCTCTCATGGAAGTTTG
TGCCTGATAATTACCACCCAGGTGACCAGCCACCTCCACCCCCTTCACATTTACGGGGCACAACATTTGCTGTGACTTTT
GGTAAAACTTCCAGAAATCCTTGGAAAGATGTCCTAGTCTGAGAAGAATCTGAAGGCTTTATTGAAACACTCTGATCTTT
TCTACAATTTTTGGCAGAATACCATGATGACTTCTTCCCAGAGTTGGCTTATGTTGCTGTCTGTGAGACATATTACAGCA
CCTAGAAACCCCCGGCAATTTAT

Alignment

ORF - retro_mmul_2362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.6 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLLNPSTPQSTESQPTTGEPATPKRRK
          P.V..YP.E.A.YKKVTSSK.FL.IKES.T...R.Q.ELSPSPPLLNPSTPQSTESQ.TT.EPAT.KR.K
Retrocopy PSVIIYP*E*ARYKKVTSSKCFLSIKESITDNKRNQGELSPSPPLLNPSTPQSTESQTTTAEPATHKRHK

Parental  AEPEALQSLRRSTRHSANSDRLSES-SASP-QPKRRQQDTSASM-PKLFLHLEKKTPVHSRSSSPIPLTP
          A.PEAL...RRST.H..N..RL.ES..ASP..P...QQ.TS.SM...L.L.LEKKTPVH.....P.P..P
Retrocopy AKPEALPAVRRSTCHITNCNRLAES<QASP<SPRCQQQATSTSM>SRLLLNLEKKTPVH--HLQPLP--P

Parental  SKEGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPS-YIYGAQHLLRLFVKLPEILGKMSFSEK
          SKE.SA.F.GFEG.RTN.INEVLSWK.VPDNY.PGDQPPPP...IYGAQHLL.L.VKLPEILGKMS.SEK
Retrocopy SKEESAAFTGFEGKRTN*INEVLSWKFVPDNYHPGDQPPPPP>HIYGAQHLL*LLVKLPEILGKMS*SEK

Parental  NLKALLKHFDL-FLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAIY
          NLKALLKH.DL.FL.FLAEYHDDFFPE.AYVA.CE..YST..P.AIY
Retrocopy NLKALLKHSDL<FLQFLAEYHDDFFPELAYVAVCETYYST*KPPAIY

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	25.21 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	21.10 RPM
SRP007412_cerebellum	0.00 RPM	18.27 RPM
SRP007412_heart	0.06 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	11.62 RPM
SRP007412_liver	0.04 RPM	4.75 RPM
SRP007412_testis	0.04 RPM	17.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2362 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2362 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362 , retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,