RetrogeneDB ID: retro_mmul_1516

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:70728675..70729570(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1838
• Ensembl ID: ENSMMUG00000008149
• Aliases: None
• Description: interleukin enhancer binding factor 2, 45kDa [Source:RefSeq peptide;Acc:NP_001253102]

Sequence

>retro_mmul_1516
ATGAGGAGTGACAAAGGTCATGGTTATGGTGGGCACTTTGGCTTCAGAAGAGTCTCAGGAGGAGAGTTCAGGCCCTTTGT
ACCACATATCTCGTTTGATTTCTATTTGTGTGAAATGGCCTTTCCCTGGGTCAAGCCCACACCTGATACAGCTTCCTTCA
ATGAGGCCTTGCTGAAGAGCAATCAGGACCCCAGCTCCTGATTCTGCTGAGCAGGCCTCTTACCTTTCCCTGGTGACAAA
AATCAACAATGTGATTGACAGTCTGATTGTGGCTCCAGGGACGTCTGAAGTGCAAATTGAAGAAGCTGGATAGGTGGGAT
CCTACAAAAAGAGAACCATCACTACAGGCCACAATGCAGCTGCCCCGCTGGTAATACGCAAGATTGTGCCAACGTTGGAA
GCTGTTGCTCCCCTGGGAAACAAAGTCGTGGGAAGCCTGAGAGCACAGGATCCTTCTGAAGTTTTGACCGTACCAACCAA
CGAAACTGGCTTTGAAATCAGTTCTTCTGATGCTACGGTGAAGACTGTCGTTACAACAGTGCCACCCAATCTTCCAAAAC
AGGACCCAGAACTCCGTTGGATATCAAGGTATTGCAGAGTGCCTTAGCAGCCATCCGGCATGCCCGCTGGTTCAAGGAAA
ATGGTTCTCAGTCCACAGTTAAAGTTCTCATCAGACTACTGAAGGACTTAAGGTTCGTCTTCCTGGCTTTGAGCCCCTCA
CACCCTGGATCCTAGGCTTACTAGGTCATTATGCTGTGATAACACCAACAGACAGCCTTTGGCCCTAAACACTGCACACA
GGTGTTGCTTGCAGATTTTGGGTGCAGGACTGTTCCTGCCAGGGTCCATGGGTATCACTGACCCCTGTGAGAGGGGCAAC
TTCAGAGTACACAGT

Alignment

ORF - retro_mmul_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.61 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRGDRGRGRGGRFGSRGGPGGGFRPFVPHIPFDFYLCEMAFPRVKPAPDETSFSEALLKRNQDL-APNSA
          MR.D.G.G.GG.FG.R...GG.FRPFVPHI.FDFYLCEMAFP.VKP.PD..SF.EALLK.NQD..AP.SA
Retrocopy MRSDKGHGYGGHFGFRRVSGGEFRPFVPHISFDFYLCEMAFPWVKPTPDTASFNEALLKSNQDP>APDSA

Parental  EQASILSLVTKINNVIDNLIVAPGTFEVQIEEVRQVGSYKKGTMTTGHNVADLVVILKILPTLEAVAALG
          EQAS.LSLVTKINNVID.LIVAPGT.EVQIEE...VGSYKK.T.TTGHN.A...VI.KI.PTLEAVA.LG
Retrocopy EQASYLSLVTKINNVIDSLIVAPGTSEVQIEEAG*VGSYKKRTITTGHNAAAPLVIRKIVPTLEAVAPLG

Parental  NKVVESLRAQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELH-LDIKVLQSALAAIRHA
          NKVV.SLRAQDPSEVLT..TNETGFEISSSDATVK...TTVPPNL.K.DPEL..LDIKVLQSALAAIRHA
Retrocopy NKVVGSLRAQDPSEVLTVPTNETGFEISSSDATVKTVVTTVPPNLPKQDPELR<LDIKVLQSALAAIRHA

Parental  RWFEENASQSTVKVLIRLLKDLR-IRFPGFEPLTPWILDLLGHYAVMNNPT-RQPLALNVAYRRCLQILA
          RWF.EN.SQSTVKVLIRLLKDLR..R.PGFEPLTPWIL.LLGHYAV...PT.RQPLALN.A.R.CLQIL.
Retrocopy RWFKENGSQSTVKVLIRLLKDLR<VRLPGFEPLTPWILGLLGHYAVI-TPT<RQPLALNTAHRCCLQILG

Parental  AGLFLPGSVGITDPCESGNFRVHT
          AGLFLPGS.GITDPCE.GNFRVH.
Retrocopy AGLFLPGSMGITDPCERGNFRVHS

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	36.42 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	43.31 RPM
SRP007412_cerebellum	0.19 RPM	42.68 RPM
SRP007412_heart	0.06 RPM	29.80 RPM
SRP007412_kidney	0.23 RPM	61.38 RPM
SRP007412_liver	0.08 RPM	23.99 RPM
SRP007412_testis	0.00 RPM	132.23 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1516 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1516 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017530	1 retrocopy	retro_cfam_1358,
Erinaceus europaeus	ENSEEUG00000013100	1 retrocopy	retro_eeur_500,
Macropus eugenii	ENSMEUG00000003651	1 retrocopy	retro_meug_1174,
Myotis lucifugus	ENSMLUG00000001847	3 retrocopies	retro_mluc_1046, retro_mluc_217, retro_mluc_2402,
Macaca mulatta	ENSMMUG00000008149	1 retrocopy	retro_mmul_1516 ,
Pan troglodytes	ENSPTRG00000001358	2 retrocopies	retro_ptro_1789, retro_ptro_963,
Ictidomys tridecemlineatus	ENSSTOG00000000667	1 retrocopy	retro_itri_130,