RetrogeneDB ID: retro_mmul_264

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 8:90513483..90514671(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000016124
• Aliases: DCAF4L2, WDR21C
• 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_264
ATGGAGAACAAAAGACCGCGACTGCTCGAGGAAGCGGACAAGCAGAAAAAGATAGCCAGAGTGGGACTCAATGCACCTTC
CATGCTACGAAAGAACCAGCTAGGTTTCCTCAGATTCGCCAACTATTGCCGTTTAGCTCGCGAGCTGCGTGTAAGCTGCA
TGCAGAGGAAAAAGGTCCAGATTCATAGCTGGGATCCCTCGTCTTTGGCAAGCGACCGATTTAACCGCATACTGGCGAAT
ACCAACACTGACCAGCTCTTCACAGTGAACCAAGTCGAAGCTGGAGGCTCCAAGTACGGCATCATCACCATGCGAGGCCT
GACGACCCCTGAACTCCGGGTATACCCGCACAAAAGCCTCTACGTCCCTAATCGGAAGGTGAATTCTATGTGCTGGGCTT
CACTGAATCACTTGGATTCCCACCTTCTGCTGTGCTTCGTGGGACTCGCAGATACTCCCAGTTGTGCCGTGCTGCTCCCA
GCGTCGCTGTTCATAGGTAGCTACCCAGGAATGCGTCGGCCAGGCATGCTCTGCAGTTTCCAGATCCCTGATGCCTGGTC
CTGTGCCTGGTCCCTGAACATCCACGCATATCACTGCTTCAGTACAGGCTTGTCTCAGCAGGTCCTGTTGACGAACGTGG
TGACGGGACATCAGCAGTCATTTGGTACTAGCAGTGATGTTTTGGCCCAGCAGTTTGCAATCATGACTCCTTTGCTGTTT
AATGGCTGTCGCTCTGGGGAGGTCTTTGGCATTGATCTGCGCTGTGGAAATCAAGGCAGGGGGTGGAAGGCCATTTGCCT
ATCCCATGATTCAGCAGTGACCTCTCTGCAAATCCTCCAAGAAGGGCAATGCCTGGTGGCATCAGACATGACTGGAACTA
TCAAGCTGTGGGACTTGAGGGCCACTAAATGTGTAACACAGTACGAAGGTCATGTGAATAACTCCGCCTACCTGCCCCTG
CATGTGAACGAGGAAGAAGGAGTCGTGGCGGCCGTGGGCCAGGACTGCTACACGAGAATCTGGAGCCTCCGTCATGGCCA
CTTGCTCACAACCATACCCTCCCCATACCCCGCCTCGGAGGATGACATTCCCAGTGTGGCCTTCTCTTCTCGCCTCGGGG
GTTTCCGAGGAGCACCAGGGCTGCTCATGGCTGTACGGGAGGACCTTTATTGTTTCTCCTACGGTTAA

Alignment

ORF - retro_mmul_264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.14 %
• Parental protein coverage: 99.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKRLRLLEEEDKQKKIARMGFNASSMLRKSQLGFLNVTSYCHLAHELRLSCMERKKVQIRSLDPSALA
          ME.KR.RLLEE.DKQKKIAR.G.NA.SMLRK.QLGFL....YC.LA.ELR.SCM.RKKVQI.S.DPS.LA
Retrocopy MENKRPRLLEEADKQKKIARVGLNAPSMLRKNQLGFLRFANYCRLARELRVSCMQRKKVQIHSWDPSSLA

Parental  SDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVNSVCWASLNHLDS
          SDRFN.ILA.TN.D.LFTVN.V..GGSKYGII....L.TP.L.V..H..LY..NRKVNS.CWASLNHLDS
Retrocopy SDRFNRILANTNTDQLFTVNQVEAGGSKYGIITMRGLTTPELRVYPHKSLYVPNRKVNSMCWASLNHLDS

Parental  HILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANNCFSTGLSRRVLL
          H.LLC..GLA.TP.CA.LLPASLF..S.PG..RPGMLCSF.IP.AWSCAWSLNI.A..CFSTGLS..VLL
Retrocopy HLLLCFVGLADTPSCAVLLPASLFIGSYPGMRRPGMLCSFQIPDAWSCAWSLNIHAYHCFSTGLSQQVLL

Parental  TNVVTGHRQSFGTNSDVLAQQFALMVPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFHDSAVTSVRILQ
          TNVVTGH.QSFGT.SDVLAQQFA.M.PLLFNGCRSGE.F.IDLRCGNQG.GWKA..L.HDSAVTS..ILQ
Retrocopy TNVVTGHQQSFGTSSDVLAQQFAIMTPLLFNGCRSGEVFGIDLRCGNQGRGWKAICLSHDSAVTSLQILQ

Parental  DEQYLMASDMAGKIKLWDLRTTKCIRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTRIWSLHDAHLLR
          ..Q.L.ASDM.G.IKLWDLR.TKC..QYEGHVN..AYLPLHV.EEEG...AVGQDCYTRIWSL...HLL.
Retrocopy EGQCLVASDMTGTIKLWDLRATKCVTQYEGHVNNSAYLPLHVNEEEGVVAAVGQDCYTRIWSLRHGHLLT

Parental  TIPSPYPASKADIPSVAFSSRLGGSRGAPGLLMAVGQDLYCYSY
          TIPSPYPAS..DIPSVAFSSRLGG.RGAPGLLMAV..DLYC.SY
Retrocopy TIPSPYPASEDDIPSVAFSSRLGGFRGAPGLLMAVREDLYCFSY

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	5.38 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	4.28 RPM
SRP007412_cerebellum	0.00 RPM	5.23 RPM
SRP007412_heart	0.12 RPM	3.53 RPM
SRP007412_kidney	0.00 RPM	11.15 RPM
SRP007412_liver	0.00 RPM	5.23 RPM
SRP007412_testis	11.80 RPM	9.27 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_264 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_264 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_264 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_92
Pan troglodytes	retro_ptro_2774
Gorilla gorilla	retro_ggor_2743

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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,