RetrogeneDB ID: retro_mmul_1414

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:12553635..12554985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCF2
• Ensembl ID: ENSMMUG00000006679
• Aliases: None
• Description: None

Sequence

>retro_mmul_1414
AGAAATAAGGCCAATGGCAGAGACACCACAGAAGTGGATTTGCTGACCAAGGAGCTAGAGGACTTTGAAATGAAGAAAGC
TGCTGCTCCAGCTGTCACTGGCATCCTGGCCTCTCATCCCAGCAGTACTGACGTTCACATTATCAACCTCTCACTCACCT
TTCACAGTCAAAAGCTGCCCAGTGACACCAAGCTGGAATTGAATTCAGGCCGTTGTTATGGCCTCATTGGCTTAAATGGA
ATTGGAAAGTTCATGCTGTTCTCTGCTATTGGGAGATGTGAAGTGCCCATCCCTGAGCACATCGACATCTACCATCTGAC
TTGAGAGATGCTCCCTAATGACAAGACACCCTTGCAGTGTGTGATGGAAGTTGACACAGAGCGGGCCATGCTGGAGAGAG
AGGCAGAGCATCTGGTTCTTGAAGATGCGGAGTGTGAGAAGCTCATGGAACTCTACGGGTACCTGGAGAAGCTGGATGCT
GATAAGGCAGAGATGAGGGCCTCGCAAATCTTGCACAGACTGGATTTCGCACCTGCCATGCAGCGCAGAAAGCTGAAAGA
CTTCAGTGGGGGCTGGAGGATGAAGGCTGCCCTTGCCAGAACCCTCTTTATTTGGCCCTTCATGCTGCTCCTGGATGAAC
CCATCAACCATCTGGACCTAGATGCTTAAATGTGGTTAGAAGAAGAACTAAAAACTTCTAAGAATATCTTGGTCCTTGTC
TCCCATTCCCAGGATTTTCTGAATGGTGTCTGTACCAACATCATTCACACGCACAAGAAACTGAAGTATTATATGGGTAA
TTATGATCAGTATGTGAAGATGCAGCTAGAACTGGAGAAGAACCAGAAGAAGAGGTTTCACTGGGAGCAAGATCAGATTG
CACACACGAAGAACTACATTGTGAGGTTTCACCATGGCAGTGGCAAGCTGGCCTGGCAGGCCCAGAGCAAGAAGAAGATG
CTAGAGAAAATGATGGCATCAGGACTGACAGAGAGGATCATGAGCGACAAGACACTGTCATTTTATTTCCCACCATATGG
CAAGATCCCTCCACCCGTCATTATGGTGCAAAATGTGAGCTTCAAGTATAAAAAAGATGGGCCTTGCATCTACAATAATC
TAGAATTTGGAATTGACCTTGACACATGAGTGGCTCTGGTAGGGCCCAACAGAGCACGGAGATCAACTCTTCTGAAGCTG
CTAACTGGAGAGCTACTACCCACAGATGGCATGATCTGAAAACACTCTTGTGTCAAGACAGGGCATTACCATCAGCATTT
ACAAGAGCAGCTGGACTTAGATATCTTGCCTTTGGAGTACATGAAGTGCTACCCAGAAATCAGGAAGAAA

Alignment

ORF - retro_mmul_1414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 72.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNEANGRETTEIDLLTKELEDFEMKKAAARAVTGVLASHPNSTDVHIINLSLTFHGQELLSDTKLELNSG
          .N.ANGR.TTE.DLLTKELEDFEMKKAAA.AVTG.LASHP.STDVHIINLSLTFH.Q.L.SDTKLELNSG
Retrocopy RNKANGRDTTEVDLLTKELEDFEMKKAAAPAVTGILASHPSSTDVHIINLSLTFHSQKLPSDTKLELNSG

Parental  RRYGLIGLNGIGKSMLLSAIGKREVPIPEHIDIYHLTREMPPSDKTPLQCVMEVDTERAMLEREAERLAH
          R.YGLIGLNGIGK.ML.SAIG..EVPIPEHIDIYHLT.EM.P.DKTPLQCVMEVDTERAMLEREAE.L..
Retrocopy RCYGLIGLNGIGKFMLFSAIGRCEVPIPEHIDIYHLT*EMLPNDKTPLQCVMEVDTERAMLEREAEHLVL

Parental  EDAECEKLMELYERLEELDADKAEMRASRILHGLGFTPAMQRKKLKDFSGGWRMRVALARALFIRPFMLL
          EDAECEKLMELY..LE.LDADKAEMRAS.ILH.L.F.PAMQR.KLKDFSGGWRM..ALAR.LFI.PFMLL
Retrocopy EDAECEKLMELYGYLEKLDADKAEMRASQILHRLDFAPAMQRRKLKDFSGGWRMKAALARTLFIWPFMLL

Parental  LDEPTNHLDLDACVWLEEELKTFKRILVLVSHSQDFLNGVCTNIIHMHNKKLKYYTVSGPRLLSESRIET
          LDEP.NHLDLDA..WLEEELKT.K.ILVLVSHSQDFLNGVCTNIIH.H.KKLKYY...............
Retrocopy LDEPINHLDLDA*MWLEEELKTSKNILVLVSHSQDFLNGVCTNIIHTH-KKLKYYMGNYDQYVKMQLELE

Parental  QVKAARLTWHISTQGNYDQYVKTARAG-GEPDEEAQSKEKTLQKMMASGLTERVVSDKTLSFYFPPCGKI
          .....R..W..........Y......G.G.....AQSK.K.L.KMMASGLTER..SDKTLSFYFPP.GKI
Retrocopy KNQKKRFHWEQDQIAHTKNYIVRFHHGSGKLAWQAQSKKKMLEKMMASGLTERIMSDKTLSFYFPPYGKI

Parental  PPPVIMVQNVSFKYTKDGPCIYNNLEFGIDLDTRVALVGPNGAGKSTLLKLLTGELLPTDGMIRKHSHVK
          PPPVIMVQNVSFKY.KDGPCIYNNLEFGIDLDT.VALVGPN.A..STLLKLLTGELLPTDGMI.KHS.VK
Retrocopy PPPVIMVQNVSFKYKKDGPCIYNNLEFGIDLDT*VALVGPNRARRSTLLKLLTGELLPTDGMI*KHSCVK

Parental  IGRYHQHLQEQLDLDLSPLEYMMKCYPEIKEK
          .G.YHQHLQEQLDLD..PLEY.MKCYPEI..K
Retrocopy TGHYHQHLQEQLDLDILPLEY-MKCYPEIRKK

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	0.56 RPM	48.97 RPM
SRP007412_brain_prefrontal_cortex	0.79 RPM	45.61 RPM
SRP007412_cerebellum	0.71 RPM	32.80 RPM
SRP007412_heart	0.29 RPM	25.26 RPM
SRP007412_kidney	0.23 RPM	22.53 RPM
SRP007412_liver	0.04 RPM	10.01 RPM
SRP007412_testis	1.39 RPM	61.74 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1414 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004830	1 retrocopy	retro_cfam_1612,
Callithrix jacchus	ENSCJAG00000020371	3 retrocopies	retro_cjac_1859, retro_cjac_3526, retro_cjac_381,
Dipodomys ordii	ENSDORG00000012672	1 retrocopy	retro_dord_334,
Echinops telfairi	ENSETEG00000008032	2 retrocopies	retro_etel_1041, retro_etel_1058,
Macaca mulatta	ENSMMUG00000006679	1 retrocopy	retro_mmul_1414 ,
Oryctolagus cuniculus	ENSOCUG00000000245	1 retrocopy	retro_ocun_765,