RetrogeneDB ID: retro_mmul_1210

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 16:4046370..4047646(+)
• Located in intron of: ENSMMUG00000005080

Retrocopy information

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

Parental gene information

• Parental gene symbol: MFSD1
• Ensembl ID: ENSMMUG00000023510
• Aliases: None
• Description: None

Sequence

>retro_mmul_1210
CTTTTGATGCTGTTATTGATGTTCTTCCTTGGCTTCAGCAGCTATTTTTGCTATAATAATCCTGCTGCCCTTCGGACTCA
GGATAAATGGGATATGCAGGTGAACACCATGCAATTCATGCTGCTATATGCCTGGTATTCTTGGCCCAGTGTGGTTTTGT
GTTTCTTTGGTCGCTTTTTAAAAGACCGAGTATTTGGAATATGATGGGGCACAATTATTTTTAGCTGTTTCATTTGCATT
GGACAGGTTGTTTTTGTTCTGAGTGGAATATTTAATGTTTTTTGGCTGATGGAATTTGAAAGATTTGTGTTTAGGATTGG
TGGGGAGTGCTTAGCAGTTGCCCAGAATACATATGCTGTGAGCTGGTTTAAAGACAAAGAATTAAACCTGGTGTTTGGAC
TCCAACAATTTAGCGTGGCTAGAATTGGAAGTACAGTAAACATGAACTTCATGAGTTGGCTGTATTCTAAGATTGAAGCT
TCGTGGGGTTCTGCTGGTCACACAACCCCTGGAGTCACACTTAAGACTGGAGGTAACATGTCTTCTTTCACTAATCTGTG
CCTTCCTTGGCTCTTGCTTACTTAGATCCCAGAGCAGAGAGAATCCTTCATAAAGAACAAAAAAAAAGGAGGGGGGGAGA
GTTTTTAAATTAACTGATGTAAAGGATTTCTCCTTACCCCTGTGGCTCATATTTATCATCTGTGTCTGCTAGCGTGTTGC
CATGTTCCCTTTTATTAGACTTGGGAAAGTTTTCTTTACGAGAAATTTGGATTTTCTTTCCAGGCAGCAAGTGCAATGAA
CAGTGTTGTGTATGTCGTATCTGCTCCCACGACCCAGTATTTGGGCTCCCGGTGGATGACACAGGGAAGAACAGCATCTG
GGTTGTGTGTGTGGTCACAGCCACTCTTGTGTCCCACATGATGCTGGCCTTTATGATGTGGAGCCCTTGGGTTGCTATGT
GTCCTCTGGGAATCTCCTAGTCATTGCCTGCCTGTGCATTATGGCCAATAGTGGCATCTGTAGTTCCTGAACATCAACTG
GGAACTGCATATGGCTTCACGCACTCCATTCAGAATCTTGGGTTGCCCATCATTTCCATCACTGCTGGGATGATACAGGA
TACTCGGGGATATTTGTTTTTTACAAGTTTTCTTCATTGCCTGTGTTTCTGTGTCACTATTATCTGTGGTCTTACTCTTA
TTTTGTGAATCATGCCCAGGGTGAGAACCTCAGTTACTCCACAAGACAAAGGGGAGAAATAAAATTTGCCCATACT

Alignment

ORF - retro_mmul_1210 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.55 %
• Parental protein coverage: 90.75 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LLVLLLMCFLGFGSYFCYDNPAALQTQVKRDMQVNTTKFMLLYAWYSWPNVVLCFFGGFLIDRVFGIRWG
          LL.LLLM.FLGF.SYFCY.NPAAL.TQ.K.DMQVNT..FMLLYAWYSWP.VVLCFFG.FL.DRVFGI.WG
Retrocopy LLMLLLMFFLGFSSYFCYNNPAALRTQDKWDMQVNTMQFMLLYAWYSWPSVVLCFFGRFLKDRVFGI*WG

Parental  TIIFSCFVCIGQVVFALGGIFNVFWLMEFGRFVFGIGGESLAVAQNTYAVSWFKGKELNLVFGLQ-LSMA
          TIIFSCF.CIGQVVF.L.GIFNVFWLMEF.RFVF.IGGE.LAVAQNTYAVSWFK.KELNLVFGLQ..S.A
Retrocopy TIIFSCFICIGQVVFVLSGIFNVFWLMEFERFVFRIGGECLAVAQNTYAVSWFKDKELNLVFGLQQFSVA

Parental  RIGSTVNMNLMGWLYSKIEALLGSAGHTTLGITLMI-GGITCILSL-ICALALAYLDQRAERILHKE--Q
          RIGSTVNMN.M.WLYSKIEA..GSAGHTT.G.TL...G.......L....LALAYLD.RAERILHKE...
Retrocopy RIGSTVNMNFMSWLYSKIEASWGSAGHTTPGVTLKTGGNMSSFTNL<VPSLALAYLDPRAERILHKEXXX

Parental  GKTGEVI-KLTDVKDFSLPLWLIFIICVCYYVAVFPFIGLGKVFFT-EKFGFSSQAASAINSVVYVISAP
          ...GE...KLTDVKDFSLPLWLIFIICVC..VA.FPFI.LGKVFFT.EKFGFS.QAASA.NSVVYV.SAP
Retrocopy XRGGEFL<KLTDVKDFSLPLWLIFIICVC*RVAMFPFIRLGKVFFT<EKFGFSFQAASAMNSVVYVVSAP

Parental  MS-PVFGLLVDKTGKNILWVLCAVAATLVSHMMLAFTMWNPWIAMCLLGLSYSLLACALWPMVAFVVPEH
          ...PVFGL.VD.TGKN..WV.C.V.ATLVSHMMLAF.MW.PW.AMC.LG.S.SL.ACALWP.VA.VVPEH
Retrocopy TT<PVFGLPVDDTGKNSIWVVCVVTATLVSHMMLAFMMWSPWVAMCPLGIS*SLPACALWPIVASVVPEH

Parental  QLGTAYGFMQSIQNLGLAIISIIAGMILDSRGYL-FLEVFFIACVSLSLLSVVLL-YLVNRAQGGNLNYS
          QLGTAYGF..SIQNLGL.IISI.AGMI.D.RGYL.FL.VFFIACVS.SLLSVVLL.Y.VN.AQG.NL.YS
Retrocopy QLGTAYGFTHSIQNLGLPIISITAGMIQDTRGYL>FLQVFFIACVSVSLLSVVLL>YFVNHAQGENLSYS

Parental  ARQREEIKFSHT
          .RQR.EIKF.HT
Retrocopy TRQRGEIKFAHT

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	0.22 RPM	42.69 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.48 RPM
SRP007412_cerebellum	0.26 RPM	24.47 RPM
SRP007412_heart	0.12 RPM	27.91 RPM
SRP007412_kidney	0.12 RPM	57.04 RPM
SRP007412_liver	0.00 RPM	19.16 RPM
SRP007412_testis	0.68 RPM	7.09 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1210 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1210 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1210 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009263	1 retrocopy	retro_btau_1323,
Dasypus novemcinctus	ENSDNOG00000005048	1 retrocopy	retro_dnov_1121,
Macaca mulatta	ENSMMUG00000023510	1 retrocopy	retro_mmul_1210 ,
Oryctolagus cuniculus	ENSOCUG00000001272	1 retrocopy	retro_ocun_1528,
Pongo abelii	ENSPPYG00000014247	1 retrocopy	retro_pabe_1427,
Tupaia belangeri	ENSTBEG00000013974	1 retrocopy	retro_tbel_1396,
Tursiops truncatus	ENSTTRG00000002207	2 retrocopies	retro_ttru_1119, retro_ttru_1271,
Drosophila melanogaster	FBgn0031636	1 retrocopy	retro_dmel_45,