RetrogeneDB ID: retro_mmul_317

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:38102795..38104337(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000000710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_317
ATGGCGGACTACCTGATCAGCGGCGGCACCCTCTACGTGCCCGAGGATGGACTCACCGCACAGCAGCTCTTCGCCAGCGC
CGACGGCCTCACCTACGACGACTTCCTGATTCTCCCAGGATTCATAGACTTCCTAACTGGTGAGGTGGACCTGACCTCAG
CCCTGACCCGGAAGATCACGCTGAAGACGCCGCTGATCTCCTTTCCCACGGACACTGTGACAGAGGCCGACATGGCCATC
GCCATGGCTCTGATGGGAGGTATTGGTTTCATTCACCACAACTGCACCCCAGAGTTCCAGGCCAACAAGGTGCAGAAAGT
CAAGAAGTTTGAACAGGGCTTCATCACAGACCCGGTGGTGCTGAGCCCCTCGCACACTGTGGGTGATGTGCTGGAGGCCA
AGGTGCGGCATGGCTTCTCTGGCATCCCCATCACTGAGACGGGCACCATGGGCAGCAAGCTAGTGGGCATCGTCACCTCC
CGAGACATCGACTTCCTTGCTGAAAAGGACCACACCACCCTCCTCAGTGAGGTGATGACGCCAAGGATCGAGCTAGTGGT
GGCTCCAGCAGGCGTGACGTTCGAAGAGGCAAATGAGATCCTGAAGCGTAGCAAGAAAGGGAAGCTGCCTGTTGTTAATG
ATCATGATGAGCTGGTGGCCATCATCGCCCGCACCAACCTGAAAAAGAACCGAGACTACCCTCTGGCCTCCAAGGATTCC
CACAAGCAGCTGCTGTGCGGGGCAGTTGTGGGCACCCGTGAAGATGACAAATTCCGCCTGGACCTGCTCACCCAGGCGGG
CGTCGATGTCATAGTCTTGGACTCGTCCCAAGGGAACTTGGTGTATCAGATCGCCATGGTGCATTACACCAAACAGAAGT
ACCCCCACCTCCAGGTGATTGGGGGGAACGTGGTGACAGCAGCCCAGGCCAAGAACCTGATTGACGCTGGTGTGGACGGG
CTGCACGTGGGCATGGGCTGCGGCTCCATCTGCATCACTCCGGAAGTGATGGCCTGTGGTCGGATCCACGGCAGTGCTGT
GTACAAGGTGGCCGAATATGCCCGGCGTTTTGGTGTCCCCATCATAGCCGATGGCGGCATCCAGACCCTGGGGCACGTGG
TCAAGGCCCTGGCCCTTGGAGCCTCCACAGTGATGATGGGCTCCCTGCTGGCCGCCACCACGGAAGCTTCTGCCGAATAC
TTCTCAGATGGGGTGCCGCTCAAGAAGTACCAGGGCATGGGCTCTCTTGATGCTATGGAGAAGAGCAGCAGTAGCCAGAA
ACGATACTTCAGCGAGGGGGATAAGGTGAAGTTCGCGCAGAGTATCTCGGGCTCTATCCGAGATAAAGGGTTCATTCAGA
AGTTCGTGCCCTACCTCATAGCGGGCATCCAGCACAGCTGCCAGGATATCGGGGCCCGCAGCCTGTCTGTCCTTCGGTCC
ATGATGTACTCAGGAGAGCTCAAGTTTGAGAAGCGGACCGTATCGGCCCAGATGGAGGGTGGCGTCCATGGCCTGCACTC
TTATGAGAAGCGGCTGTACTGA

Alignment

ORF - retro_mmul_317 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 90.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFLILPGFIDFIADEVDLTSALTRKITLKTPLISSPMDTVTEADMAIAMALMGGIGFIHHNCTPEFQANE
          DFLILPGFIDF...EVDLTSALTRKITLKTPLIS.P.DTVTEADMAIAMALMGGIGFIHHNCTPEFQAN.
Retrocopy DFLILPGFIDFLTGEVDLTSALTRKITLKTPLISFPTDTVTEADMAIAMALMGGIGFIHHNCTPEFQANK

Parental  VRKVKKFEQGFITDPVVLSPSHTVGDVLEAKMRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTT
          V.KVKKFEQGFITDPVVLSPSHTVGDVLEAK.RHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTT
Retrocopy VQKVKKFEQGFITDPVVLSPSHTVGDVLEAKVRHGFSGIPITETGTMGSKLVGIVTSRDIDFLAEKDHTT

Parental  LLSEVMTPRIELVVAPAGVTLKEANEILQRSKKGKLPIVNDRDELVAIIARTDLKKNRDYPLASKDSHKQ
          LLSEVMTPRIELVVAPAGVT..EANEIL.RSKKGKLP.VND.DELVAIIART.LKKNRDYPLASKDSHKQ
Retrocopy LLSEVMTPRIELVVAPAGVTFEEANEILKRSKKGKLPVVNDHDELVAIIARTNLKKNRDYPLASKDSHKQ

Parental  LLCGAAVGTREDDKYRLDLLTQAGVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNL
          LLCGA.VGTREDDK.RLDLLTQAGVDVIVLDSSQGN.VYQIAMVHY.KQKYPHLQVIGGNVVTAAQAKNL
Retrocopy LLCGAVVGTREDDKFRLDLLTQAGVDVIVLDSSQGNLVYQIAMVHYTKQKYPHLQVIGGNVVTAAQAKNL

Parental  IDAGVDGLRVGMGCGSICITQEVMACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKALALGAST
          IDAGVDGL.VGMGCGSICIT.EVMACGR..G.AVYKVAEYARRFGVPIIADGGIQT.GHVVKALALGAST
Retrocopy IDAGVDGLHVGMGCGSICITPEVMACGRIHGSAVYKVAEYARRFGVPIIADGGIQTLGHVVKALALGAST

Parental  VMMGSLLAATTEAPGEYFFSDGVRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSI
          VMMGSLLAATTEA..EY.FSDGV.LKKY.GMGSLDAMEKSSSSQKRYFSEGDKVK.AQ..SGSI.DKG.I
Retrocopy VMMGSLLAATTEASAEY-FSDGVPLKKYQGMGSLDAMEKSSSSQKRYFSEGDKVKFAQSISGSIRDKGFI

Parental  QKFVPYLIAGIQHGCQDIGARSLSVLRSMMYSGELKFEKRTMSAQIEGGVHGLHSYEKRLY
          QKFVPYLIAGIQH.CQDIGARSLSVLRSMMYSGELKFEKRT.SAQ.EGGVHGLHSYEKRLY
Retrocopy QKFVPYLIAGIQHSCQDIGARSLSVLRSMMYSGELKFEKRTVSAQMEGGVHGLHSYEKRLY

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	0.22 RPM	10.42 RPM
SRP007412_brain_prefrontal_cortex	0.08 RPM	26.34 RPM
SRP007412_cerebellum	0.19 RPM	8.85 RPM
SRP007412_heart	0.00 RPM	11.95 RPM
SRP007412_kidney	0.00 RPM	9.62 RPM
SRP007412_liver	0.16 RPM	16.59 RPM
SRP007412_testis	2.49 RPM	9.57 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_317 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_317 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_317 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4808
Pan troglodytes	retro_ptro_3198
Gorilla gorilla	retro_ggor_2993
Pongo abelii	retro_pabe_3736

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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,