RetrogeneDB ID: retro_mmul_972

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 12:97748872..97750114(-)
• Located in intron of: None

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_972
TTAAAAGGCCTTTCCATCGAAGAAAGAGATGAAAATGATGAAAACTCATTAAGCAGTTCCTCCGACAGTAGTGAAGACAA
GGATGAAAAAATAAGTGAAGAAAGTGATACTGAAGAAAAGGCTGAAGTAAAGGAAGAACCGGAGCTTCAAACAAAAAGGG
AAATGGAAGAAAGAACAGTAACTCTAGAAATCCCTGAAGTTTTGAAGAGGCAGCTGGAGGATGATTGTTACTACATTAAT
CGGAGGAAACGGTTAGTGAAACTTCCATGCCACACCAACATCATAACGATTTTGGAATCCTATGTGAGGCATTTTGCTAT
CAGTGCAGCCTTTTCAGCCAATGAGCGGCCTCGTCACCTTCACGCTATGCCACATGCCAACATGAATGTGCCTTATATCC
CAGCAGAAAAGAATGTTGACCTTTGTAAGGAGATGGCGGATGGATTAAGAATAACTTTTGATTACACTCTCCCGTTGGTT
TTACTCTATCCCTATGAACAAGCTCAGTATAAAAAGGTGACTGCATCTAAGGTTTTTCTTGCAATTAAGGAAAGTGCCAC
AAATACTAGTAGGAGCCAGGAGAAGCTCTGTCCCAGAGAGAGAGATTTGTTGAATCCATCCAGGCCGCAGTCTACAGAGA
GTCCGTCAACCACTGGTGAACGAGCCACCCCCAAAAGGCGCAAAGCCGAGCCGGAAGCAGTGCGGTCTCTGAGGCGGTCC
TCGCCCCACACGGCCAACTGTGACAGGCTTTCTAAGACCAGCACCTCACCTCAGCCCAAGCGCTGGCAGCAGGACATGTC
CACCAGCATGCCCAAGCTGTTCCTGCACCTGGAAAAGAAGACACCTGTGCATAGCAGATCATCTTCACCTATTCCTCTGA
CTCCTAACCAGAGTCAGGGAATAGAAGGGAGTGCTGCGTTTGCTGGCTTTGAAGGGAGAAGAACTAATGAAATAAATGAG
GTCCTCTCCTGGAAGCTCGTGCCTGACAATTACCCACCAGGTGACCAGGCGCCTCCACCCTCTTACATTTACGGGGCGCA
ACATTTGCTGCGATTGTTTGTAAAACTTCCAGAAATTCTTGGAAAAATGTCCTTTGCTGAGAAGAATCTGAAGGCTTTAT
TGAAGCACTTTGATCTCTTTGTGAGGTTTTTAGCAGAATACCACGATGACTTCTTCCCAGAGTCGGCTTATGTCGCTGCC
TCTGAGGTGCATTACAGCACCAAGAACTCCCAGGCAGCCTAT

Alignment

ORF - retro_mmul_972 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.75 %
• Parental protein coverage: 84.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKGLPTEEKDENDENSLSSSSDCSEDKDEEISEESDIEEKTEVKEEPELQTKREMEERTITIEIPEVLKK
          LKGL..EE.DENDENSLSSSSD.SEDKDE.ISEESD.EEK.EVKEEPELQTKREMEERT.T.EIPEVLK.
Retrocopy LKGLSIEERDENDENSLSSSSDSSEDKDEKISEESDTEEKAEVKEEPELQTKREMEERTVTLEIPEVLKR

Parental  QLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANERPRHHHVMPHANMNVHYIPAEKNVD
          QLEDDCYYINRRKRLVKLPC.TNIITILESYV.HFAI.AAFSANERPRH.H.MPHANMNV.YIPAEKNVD
Retrocopy QLEDDCYYINRRKRLVKLPCHTNIITILESYVRHFAISAAFSANERPRHLHAMPHANMNVPYIPAEKNVD

Parental  LCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSP-SPPLLNPSTPQ
          LCKEM.DGLRITFDYTLPLVLLYPYEQAQYKKVT.SK.FL.IKESAT.T.RSQE.L.P....LLNPS.PQ
Retrocopy LCKEMADGLRITFDYTLPLVLLYPYEQAQYKKVTASKVFLAIKESATNTSRSQEKLCPRERDLLNPSRPQ

Parental  STESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANSDRLSESSASPQPKRRQQDTSASMPKLFLHLEKK
          STES..TTGE.ATPKRRKAEPEA..SLRRS..H.AN.DRLS..S.SPQPKR.QQD.S.SMPKLFLHLEKK
Retrocopy STESPSTTGERATPKRRKAEPEAVRSLRRSSPHTANCDRLSKTSTSPQPKRWQQDMSTSMPKLFLHLEKK

Parental  TPVHSRSSSPIPLTPSK----EGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLL
          TPVHSRSSSPIPLTP......EGSA.FAGFEGRRTNEINEVLSWKLVPDNYPPGDQ.PPPSYIYGAQHLL
Retrocopy TPVHSRSSSPIPLTPNQSQGIEGSAAFAGFEGRRTNEINEVLSWKLVPDNYPPGDQAPPPSYIYGAQHLL

Parental  RLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAIY
          RLFVKLPEILGKMSF.EKNLKALLKHFDLF.RFLAEYHDDFFPESAYVAA.E.HYSTKN..A.Y
Retrocopy RLFVKLPEILGKMSFAEKNLKALLKHFDLFVRFLAEYHDDFFPESAYVAASEVHYSTKNSQAAY

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	2.13 RPM	25.21 RPM
SRP007412_brain_prefrontal_cortex	1.59 RPM	21.10 RPM
SRP007412_cerebellum	1.36 RPM	18.27 RPM
SRP007412_heart	0.65 RPM	6.65 RPM
SRP007412_kidney	0.82 RPM	11.62 RPM
SRP007412_liver	0.95 RPM	4.75 RPM
SRP007412_testis	18.17 RPM	17.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_972 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_972 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_972 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,