RetrogeneDB ID: retro_mmul_818

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:67624821..67625762(+)
• Located in intron of: ENSMMUG00000011075

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAHD2B
• Ensembl ID: ENSMMUG00000012859
• Aliases: None
• Description: None

Sequence

>retro_mmul_818
ATGCTGGTCTCTGGTAGAAGAAGGCTGCTCACAGCTCTGCTGCAGGCTCAGAAGTGGCCCTTTCAACCCTCCAGAGACAT
AAGACTAGTGCAGTTCCAGGCACCCCACCTGGTGGGGCCTCACTTTGGCCTGGAGACGGGGAATGGTGGAGGGGTTATCA
ACCGCAATGCCTTTGACTCTATGCTCCCCAAGATGATGACACAGTTCCTAGAGCAGGGAGAGGCCACCCTTTCAGTGGCA
AGAAGAGCCTTGGGTACCCAGTTGCCAGTCCTATCACGGTTGGAAGTAACCTTCCTGGCTCCAGCTACGTGGCCAGATAA
GGTGCTTTGTGTGGGCATGAATTATGTGGACCACTGCAAAGAACAGAACATGCCTGTGCCCATGGAACCCATTATCTTCA
GCAAGTTTGCCAACTCCATCGTGGAGTCCTATGATGAGATGGTCCTCCCACTGGAGAGCCAGGACGTAGACTGGGAAGTG
GAGTGGCCGTGGTCACTGGAAAGAAAGGCAAGCACGTCAAGGCCACAGATGCCATGGCCCATGTGGCTGGCTTCACTATG
GCTAATGACGTGAGTGCTCATGACTGGCAAATGAGACATAAGGGGAAACAGTGGCTGCTGGGAAAAACCTTCGACACCTT
CTGCCCCCTGGGCCCGGCCTTGGTAACCAAGGACAGTGTAGCAGATCCACACAACTTGAAGATCTGCTGCCAAGTGAACG
GGGAAGTGGTCCAGAGCAGCAACACCAACCAGATGGTGGTTAAGACAGAGGAACTGACAGCCTGGGTCTCCCAGTTTGTC
ACCTTTTACCCAGGGGATGTCATCCTGACTGGGACCTCCCCAGGTGTCGTTGTATTCAGGAAATCTCCTGTCCTTCTCAA
GAAGGGGGATAAAGTCCAGTGTGAGACTGAAGAACTAGGTGTCATCATCAGCTAGGTGGTG

Alignment

ORF - retro_mmul_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.76 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVSGRRRLLTALLQAQKWPFQPSRDMRLVQFQAPHLVGPHLGLETGNGGGVINLNAFDPTLPKTMTQFL
          MLVSGRRRLLTALLQAQKWPFQPSRD.RLVQFQAPHLVGPH.GLETGNGGGVIN.NAFD..LPK.MTQFL
Retrocopy MLVSGRRRLLTALLQAQKWPFQPSRDIRLVQFQAPHLVGPHFGLETGNGGGVINRNAFDSMLPKMMTQFL

Parental  EQGEATLSVARRALAAQLPVLPRSEVTFLAPVTRPDKVVCVGMNYADHCKEQNVPVPKEPIIFSKFASSI
          EQGEATLSVARRAL..QLPVL.R.EVTFLAP.T.PDKV.CVGMNY.DHCKEQN.PVP.EPIIFSKFA.SI
Retrocopy EQGEATLSVARRALGTQLPVLSRLEVTFLAPATWPDKVLCVGMNYVDHCKEQNMPVPMEPIIFSKFANSI

Parental  VGPYDEVVLPPESQEVDWEAE-LAVVIGKKGKHIKATDAMAHVAGFTVAHDVSARDWLTTRNGKQWLLGK
          V..YDE.VLP.ESQ.VDWE.E..AVV.GKKGKH.KATDAMAHVAGFT.A.DVSA.DW.....GKQWLLGK
Retrocopy VESYDEMVLPLESQDVDWEVE<VAVVTGKKGKHVKATDAMAHVAGFTMANDVSAHDWQMRHKGKQWLLGK

Parental  TFDTFCPLGPALVTKDSVADPHNLKICCRVNGEVVQSSNTNQMVFKTEDLIAWVSQFVTFYPGDVILTG-
          TFDTFCPLGPALVTKDSVADPHNLKICC.VNGEVVQSSNTNQMV.KTE.L.AWVSQFVTFYPGDVILTG.
Retrocopy TFDTFCPLGPALVTKDSVADPHNLKICCQVNGEVVQSSNTNQMVVKTEELTAWVSQFVTFYPGDVILTGT

Parental  PPGVGVFRKPPVFLKKGDEVQCEIEELGVIINKVV
          .PGV.VFRK.PV.LKKGD.VQCE.EELGVII..VV
Retrocopy SPGVVVFRKSPVLLKKGDKVQCETEELGVIIS*VV

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	0.45 RPM	10.76 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	20.94 RPM
SRP007412_cerebellum	0.97 RPM	7.88 RPM
SRP007412_heart	0.47 RPM	13.01 RPM
SRP007412_kidney	1.29 RPM	20.30 RPM
SRP007412_liver	0.79 RPM	29.29 RPM
SRP007412_testis	0.64 RPM	8.86 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_818 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_818 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1025
Pan troglodytes	retro_ptro_700
Gorilla gorilla	retro_ggor_810
Pongo abelii	retro_pabe_860

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018863	1 retrocopy	retro_cjac_3222,
Homo sapiens	ENSG00000144199	1 retrocopy	retro_hsap_1025,
Gorilla gorilla	ENSGGOG00000016246	1 retrocopy	retro_ggor_810,
Macaca mulatta	ENSMMUG00000012859	1 retrocopy	retro_mmul_818 ,
Nomascus leucogenys	ENSNLEG00000000008	1 retrocopy	retro_nleu_903,
Pongo abelii	ENSPPYG00000012057	1 retrocopy	retro_pabe_860,
Pan troglodytes	ENSPTRG00000012214	1 retrocopy	retro_ptro_700,