RetrogeneDB ID: retro_mmul_152

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:37024645..37025836(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000022781
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSMMUG00000003625
• Aliases: DCAF4, WDR21A
• Description: DDB1- and CUL4-associated factor 4 [Source:RefSeq peptide;Acc:NP_001245043]

Sequence

>retro_mmul_152
ATGGAGGCGGAAAGGCTGCGACTCCTCGAGGAGGAGGCCAAGCAGAAAAAGGTAGCCAGAATGGGATTTAATGCATCTTC
TATGCTCCGAAAAAGCCAGCTAGGTTTCCTCAACGTCACCAGTTACTCCCGTTTAGCCAACGAGCTGCGTGTGAGCTGCA
TGGAGAGAAAAAAAGTCCAGATTCGGAGCTTGGATCCCTCCTCTTTGGCGACCGACCGATTTAACTTCATTCTGGCGAGT
ACCAACAGCGACCAGCTCTTCGTAGTGAACCAGGTCGAAGTCGAAGGCTCCAAGTACGGCATTATCAGCCTGCGAACTCT
GAAGATCCCTTCATTCCACGTGTACGTGCTCAGAAACCTCTACGTCCCCAACCGGAAGGTGAAGTCCCTGTGCTGGGCCT
CGCTGAACCAGTTGGACTCTCACATTCTGCTGTGCTTCGAGGGAATTACAGATGCTCCAAGCTGTGCGGTGCTGCTCCCA
GCGTCGCGATTCTTAAGTGTTCACACAAGAGTAAACCAGCCTGGCATGCTCTGCAGTTTCCAGATCCCTGAGGCCTGGTC
CTGTGCCTGGTCCCTCAACACCCGGGCATATCACTGCTTTAGTGCAGGCTTGTCTCAGCAGGTCCTGTTGACCAACGTGG
CGACGGGACACCAGCAGTCGTTTGGTGCCAGCAGTGATGTCTTGGCCCAGCAATTTGCTAGTACGGCTCCTTTGCTGTTT
AATGGCTGTCGCTCCGGGGAGATCTTTGCCATTGATCTGCGCTGTAGAAATCGAGGCAAGGGGTGGAGGGCCACTCGCCT
GTTCCATGACTCTGCAGTGACCTCTGTGCAAATCCTCCAAGAAGAGCAATGCCTGATGGCGTCAGACATGACTGGAAAGA
TCAAGCTGTGGGATCTGAGGGCCACTAAATGTTTAAGGCAGTACGAAGGTCACGTGAATGAGTCCGCCTATCTGCCCCTG
CATGTGCACGAGGAAGAGGGAATCGTGGTGGCAGTGGGCCAGGACTGCTACACGAGAATCTGGAGCCTCCATGATGCCCA
CCTGCTCAGAACCATCCCTTCCCCGTATTCTGCCTCCGAGGACGACATTCCCAGCGTGGCCTTCGCTTCTCGGCTCGGGG
GCATCCGGGGAGCAGCACCAGGGCTGCTCATGGCTGTCCGGCAGGACCTTTATTGTTTCCCCTTCAGCTAA

Alignment

ORF - retro_mmul_152 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKRLRLLEEEDKQKKIARMGFNASSMLRKSQLGFLNVTSYCHLAHELRLSCMERKKVQIRSLDPSALA
          ME..RLRLLEEE.KQKK.ARMGFNASSMLRKSQLGFLNVTSY..LA.ELR.SCMERKKVQIRSLDPS.LA
Retrocopy MEAERLRLLEEEAKQKKVARMGFNASSMLRKSQLGFLNVTSYSRLANELRVSCMERKKVQIRSLDPSSLA

Parental  SDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVNSVCWASLNHLDS
          .DRFN.ILA.TNSD.LF.VN.V.V.GSKYGII.L..LK.P...V....NLY..NRKV.S.CWASLN.LDS
Retrocopy TDRFNFILASTNSDQLFVVNQVEVEGSKYGIISLRTLKIPSFHVYVLRNLYVPNRKVKSLCWASLNQLDS

Parental  HILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANNCFSTGLSRRVLL
          HILLC..G....P.CA.LLPAS.F...H.....PGMLCSF.IP.AWSCAWSLN..A..CFS.GLS..VLL
Retrocopy HILLCFEGITDAPSCAVLLPASRFLSVHTRVNQPGMLCSFQIPEAWSCAWSLNTRAYHCFSAGLSQQVLL

Parental  TNVVTGHRQSFGTNSDVLAQQFALMVPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFHDSAVTSVRILQ
          TNV.TGH.QSFG..SDVLAQQFA...PLLFNGCRSGEIFAIDLRC.N.GKGW.ATRLFHDSAVTSV.ILQ
Retrocopy TNVATGHQQSFGASSDVLAQQFASTAPLLFNGCRSGEIFAIDLRCRNRGKGWRATRLFHDSAVTSVQILQ

Parental  DEQYLMASDMAGKIKLWDLRTTKCIRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTRIWSLHDAHLLR
          .EQ.LMASDM.GKIKLWDLR.TKC.RQYEGHVNE.AYLPLHVHEEEGI.VAVGQDCYTRIWSLHDAHLLR
Retrocopy EEQCLMASDMTGKIKLWDLRATKCLRQYEGHVNESAYLPLHVHEEEGIVVAVGQDCYTRIWSLHDAHLLR

Parental  TIPSPYPASKADIPSVAFSSRLGGSRG-APGLLMAVGQDLYCYSYS
          TIPSPY.AS..DIPSVAF.SRLGG.RG.APGLLMAV.QDLYC...S
Retrocopy TIPSPYSASEDDIPSVAFASRLGGIRGAAPGLLMAVRQDLYCFPFS

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	0.90 RPM	5.38 RPM
SRP007412_brain_prefrontal_cortex	0.87 RPM	4.28 RPM
SRP007412_cerebellum	0.77 RPM	5.23 RPM
SRP007412_heart	0.12 RPM	3.53 RPM
SRP007412_kidney	1.06 RPM	11.15 RPM
SRP007412_liver	0.16 RPM	5.23 RPM
SRP007412_testis	8.86 RPM	9.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_152 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_152 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_101
Pan troglodytes	retro_ptro_46
Gorilla gorilla	retro_ggor_2026

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013878	1 retrocopy	retro_cpor_293,
Homo sapiens	ENSG00000119599	2 retrocopies	retro_hsap_101, retro_hsap_92,
Gorilla gorilla	ENSGGOG00000003815	2 retrocopies	retro_ggor_2026, retro_ggor_2743,
Macaca mulatta	ENSMMUG00000003625	2 retrocopies	retro_mmul_152 , retro_mmul_264,
Nomascus leucogenys	ENSNLEG00000002449	2 retrocopies	retro_nleu_1912, retro_nleu_833,
Pan troglodytes	ENSPTRG00000006507	2 retrocopies	retro_ptro_2774, retro_ptro_46,