RetrogeneDB ID: retro_mmul_1551

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 20:10228731..10229615(+)
• Located in intron of: ENSMMUG00000010142

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSMMUG00000014509
• Aliases: None
• Description: IMP (inosine 5'-monophosphate) dehydrogenase 1 [Source:HGNC Symbol;Acc:6052]

Sequence

>retro_mmul_1551
TCTCCCCCCATGGACACTGAGACAGAGGCCAACATGGCCATAGCGATGGCTCTGATGGGAGGTACTGGTTTCATTCACCA
CAGCTGTACCCCAGGGTTCCAGGCCAACGAGGTACGTAAGGTCAAGAAGTTTGAACAGGGCTTCATCACGGACCCTGTGG
TGCTGAGCCCCTCGCACACTGTGGGTGATGAGCTGGAAGCCAAGATCCAGCATGGCTTCTCTGGCATTCCCATCACTGAG
ACAGGCACCATGGGCAGCAAGCTGGTGGGCATCGTCACCTCCCAAGACATCGACTTTCTTGCTGAGAAGGACCACACCAG
CCTCCTCAGTGAGGTGATGAAGCCAAGGATCAAGCCGATGGTGGTTCCAACAGGTGTGACATTGAAAGAGGCAAATGAGA
TCCTTCAGGGTAGCAAGAAAGGGAAGCTGCCTATAGTCAATGATCGCCATGAGCTAGTGGCCATCATCGCCCACACCAAT
CTGAAGAACCGAGACTACCCTCTGATCTCCAAGGATTCCCCAAGCACCTGCTGCACTGGGCAGCTGTGAGCACCCATGAG
GATGACAAATACCGCCTGGACCTGCTCACCTGGGTAGGCGTCAATGTCATAGTCTTGGACTCCTCCCAAGGGAACTGGGT
CTATCAAATCACCATGGTGCATTACATCAAACAGAAGTACCCCCACCTCCAGGTGATTGGGAGGAATGTGGTGACAGCAG
CCCAGGCCAAGAATCTGATTGATGCTGGTGTGGACGGACTGCACGTGGGCATGGGCTGCAGCTCCATCTGCATCACCCAG
GAAGTGATGGCCTGAGGTCGGCCCCAGGGCACTGCTGCGTATAAGGTGGCCAAGTATGCCCAGCACTTTGGTGTGTCCAT
CATA

Alignment

ORF - retro_mmul_1551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANEVRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMR
          S.PMDT.TEA.MAIAMALMGG.GFIHH.CTP.FQANEVRKVKKFEQGFITDPVVLSPSHTVGD.LEAK..
Retrocopy SPPMDTETEANMAIAMALMGGTGFIHHSCTPGFQANEVRKVKKFEQGFITDPVVLSPSHTVGDELEAKIQ

Parental  HGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTTLLSEVMTPRIELVVAPAGVTLKEANEILQRSKK
          HGFSGIPITETGTMGSKLVGIVTS.DIDFLAEKDHT.LLSEVM.PRI...V.P.GVTLKEANEILQ.SKK
Retrocopy HGFSGIPITETGTMGSKLVGIVTSQDIDFLAEKDHTSLLSEVMKPRIKPMVVPTGVTLKEANEILQGSKK

Parental  GKLPIVNDRDELVAIIARTDLKKNRDYPLASKDS-HKQLLCGAAVGTREDDKYRLDLLTQAGVDVIVLDS
          GKLPIVNDR.ELVAIIA.T.L.KNRDYPL.SKDS..K.LL..AAV.T.EDDKYRLDLLT..GV.VIVLDS
Retrocopy GKLPIVNDRHELVAIIAHTNL-KNRDYPLISKDS<PKHLLHWAAVSTHEDDKYRLDLLTWVGVNVIVLDS

Parental  SQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEVMACGRPQGT
          SQGN.VYQI.MVHYIKQKYPHLQVIG.NVVTAAQAKNLIDAGVDGL.VGMGC.SICITQEVMA.GRPQGT
Retrocopy SQGNWVYQITMVHYIKQKYPHLQVIGRNVVTAAQAKNLIDAGVDGLHVGMGCSSICITQEVMA*GRPQGT

Parental  AVYKVAEYARRFGVPII
          A.YKVA.YA..FGV.II
Retrocopy AAYKVAKYAQHFGVSII

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	10.42 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	26.34 RPM
SRP007412_cerebellum	0.45 RPM	8.85 RPM
SRP007412_heart	0.00 RPM	11.95 RPM
SRP007412_kidney	0.00 RPM	9.62 RPM
SRP007412_liver	0.00 RPM	16.59 RPM
SRP007412_testis	0.08 RPM	9.57 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1551 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1551 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1087

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017770	1 retrocopy	retro_cjac_2045,
Homo sapiens	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
Gorilla gorilla	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798, retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
Macropus eugenii	ENSMEUG00000016082	2 retrocopies	retro_meug_2095, retro_meug_542,
Macaca mulatta	ENSMMUG00000014509	2 retrocopies	retro_mmul_1551 , retro_mmul_317,
Nomascus leucogenys	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
Pongo abelii	ENSPPYG00000017976	7 retrocopies	retro_pabe_2133, retro_pabe_2138, retro_pabe_2346, retro_pabe_3102, retro_pabe_3292, retro_pabe_3392, retro_pabe_3736,
Pan troglodytes	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,