RetrogeneDB ID: retro_mmul_1523

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:90501450..90502305(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRBF2
• Ensembl ID: ENSMMUG00000017726
• Aliases: None
• Description: nuclear receptor-binding factor 2 [Source:RefSeq peptide;Acc:NP_001248660]

Sequence

>retro_mmul_1523
ATGGAAGTAATGGAAGGACCCCTTAACCTGGCTCATCAACAGAGCAGACGAGCAGACCGTTTATTAGCTGCAGGCAAATA
CGAAGAGGCTATTTCTTGTCACAAAAAGGCTGCGGCATATCTTTCTGAAGCCATGAAGCTGACACAGTCTGAGCAGGCTC
ATCTTTCACTGGAACTGCAAAAGGATAGCCACATGAAACAGCTCCTCCTCATCCAAGAGAGATGGAAAAGGGCCCAGCGT
GAGGAAAGATTGAAAGCCTAGCAGAACACAGACAAGGATGTGGCTACCCATATTCAGGCATCTCACAAACCCTCTGCCGA
GGATGCGGAGGGCCAGAGCCCCATTTCTCAGTACAGTACTTCCTCAGAGAAACGCTTGCCTGAAATTCAGCGGATCTTTG
GCAAGGATCCAGACACACTGCTATATTTACTTCAGCAAAAGAGTGAGCCAGCAGCGCTATGTATTGGAAGCAAAGCCCCA
GAAGATGATAAATCAAATATAGAGGAGCAGGCAACCAAAATTGCAGATTTGAAGAGGCATGTGGAATTCCTTGTAGCTGA
GAATGAAAGATTAAGGAAAGAAAATAACTAAAGGCTGAAAAGGCCAGACTTCTAAAAAGGTCCAGTAGAAAAGGAGCTGG
ATGTAGGTGCTAATTTTGTAGAAATGTCAGTGTTACGGAGCTTGCCATCACATTCAGAAACTGCTACAGCCTCCTCAACC
TGGCGGAAGTTTGCAGCAAATGCCGGGAAAGCCAAAGACATTCCAATCCCCAATTTTCCTCCCTTGGATTTTACATCTCC
AGAACTTCCCCTTATGGAACTTCCTGAGAATATTCTGAAAGGATTTATTAATAAT

Alignment

ORF - retro_mmul_1523 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLL
          MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQ.DSHMKQLLL
Retrocopy MEVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQKDSHMKQLLL

Parental  IQERWKRAQREERLKAQQNTDKDVAAHLQASHKPSAEDAEGQSPLSQKYSPSTEKCLPEIQGIFDRDPDT
          IQERWKRAQREERLKA.QNTDKDVA.H.QASHKPSAEDAEGQSP.SQ.YS.S.EK.LPEIQ.IF..DPDT
Retrocopy IQERWKRAQREERLKA*QNTDKDVATHIQASHKPSAEDAEGQSPISQ-YSTSSEKRLPEIQRIFGKDPDT

Parental  LLYLLQQKSEPAEPCIGSKAPKDDKTIIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLLKGP
          LLYLLQQKSEPA..CIGSKAP.DDK..IEEQATKIADLKRHVEFLVAENERLRKEN...........KGP
Retrocopy LLYLLQQKSEPAALCIGSKAPEDDKSNIEEQATKIADLKRHVEFLVAENERLRKEN-N*RLKRPDF*KGP

Parental  IEKELDVDADFVETSELWSLPPHSETATASSTWQKFAANTGKAKDIPIPNLPPLDFPSPELPLMELSEDI
          .EKELDV.A.FVE.S.L.SLP.HSETATASSTW.KFAAN.GKAKDIPIPN.PPLDF.SPELPLMEL.E.I
Retrocopy VEKELDVGANFVEMSVLRSLPSHSETATASSTWRKFAANAGKAKDIPIPNFPPLDFTSPELPLMELPENI

Parental  LKGFMSN
          LKGF..N
Retrocopy LKGFINN

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	12.89 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	10.23 RPM
SRP007412_cerebellum	0.06 RPM	10.78 RPM
SRP007412_heart	0.00 RPM	5.83 RPM
SRP007412_kidney	0.00 RPM	8.57 RPM
SRP007412_liver	0.00 RPM	14.01 RPM
SRP007412_testis	1.32 RPM	5.28 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1523 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1523 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1523 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2643
Pan troglodytes	retro_ptro_1780
Pongo abelii	retro_pabe_2327

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004648	3 retrocopies	retro_chof_1032, retro_chof_2250, retro_chof_2568,
Homo sapiens	ENSG00000148572	3 retrocopies	retro_hsap_2643, retro_hsap_3999, retro_hsap_433,
Gorilla gorilla	ENSGGOG00000013016	2 retrocopies	retro_ggor_1846, retro_ggor_2685,
Macropus eugenii	ENSMEUG00000010849	3 retrocopies	retro_meug_1385, retro_meug_2049, retro_meug_671,
Macaca mulatta	ENSMMUG00000017726	1 retrocopy	retro_mmul_1523 ,
Monodelphis domestica	ENSMODG00000017183	1 retrocopy	retro_mdom_1995,
Mus musculus	ENSMUSG00000075000	2 retrocopies	retro_mmus_1278, retro_mmus_1279,
Otolemur garnettii	ENSOGAG00000005856	1 retrocopy	retro_ogar_2110,
Pongo abelii	ENSPPYG00000002411	3 retrocopies	retro_pabe_2327, retro_pabe_3285, retro_pabe_3286,
Pan troglodytes	ENSPTRG00000002539	3 retrocopies	retro_ptro_1780, retro_ptro_194, retro_ptro_2715,
Rattus norvegicus	ENSRNOG00000000641	2 retrocopies	retro_rnor_1681, retro_rnor_994,
Sarcophilus harrisii	ENSSHAG00000004744	1 retrocopy	retro_shar_427,
Ictidomys tridecemlineatus	ENSSTOG00000011341	1 retrocopy	retro_itri_183,