RetrogeneDB ID: retro_ptro_46

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:42050549..42051740(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000031217
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSPTRG00000006507
• Aliases: DCAF4, WDR21A
• Description: None

Sequence

>retro_ptro_46
ATGGAGGCTGAAAGGCTGCGACTCCTCGAGGAAGAGGCCAAGCTGAAAAAGGTAGCCAGAATGGGATTTAATGCATCTTC
CATGCTCCGAAAAAGCCAGCTAGGTTTCCTCAACGTCACCAGTTACTCCCGTTTAGCCAACGAGCTGCGTGTGAGCTGCA
TGGAGCGGAAAAAGGTCCAAATTCGGAGCTTGGATCCCTCCTCTTTGGCGAGCGACCGATTTAACTTCATTCTGGCGAGT
ACCAACAGCGACCAGCTTTTCGTAGTGAACCAGGTCGAAGTCGAAGGCTCCAAGTACGGCATCATCAGCCTGCGAACTCT
GAAGATCCCTTCGTTCCACGTGTACGTGCTCAGAAACCTCTACGTCCCCAACCGGAAGGTGAAGTCCCTGTGCTGGGCCT
CGCTGAACCAGTTGGACTCTCACATTCTGCTGTGCTTCGAGGGAATCACAGATGCTCCAAGCTGTGCAGTGCTGCTCCCA
GCGTCGCGGTTCTTAAGTGTTCACACGAGAGTTAACCAGCCTGGCATGCTCTGCAGTTTCCAGATCCCAGAGGCCTGGTC
CTGTGCGTGGTCCCTCAACACCCGGGCATATCACTGCTTTAGTGCAGGCTTGTCTCGGCAGGTCCTGTTGACCAGCGTGG
CGACGGGACACCAGCAGTCATTTGATACCAGCAGTGATGTCTTGGCCCAGCAGTTTGCTAATACGGCTCCTTTGCTGTTT
AATGGCTGTCGCTCCGGGGAGATCTTTGCCATTGATCTGCGTTGTAGAAATCGAGGCAAGGGGTGGAGGGCCACTCGCCT
GTTCCATGACTCAGCAGTGACCTCTGTGCAAATCCTCCAAGAAGAGCAATGCCTGATGGCATCAGACATGACTGGAAAGA
TCAAGCTGTGGGATCTGAGGGCCACTAAATGTGTAAGGCAGTACGAAGGTCACGTGAATGAGTCCGCCTATCTGCCCCTG
CATGTGCACGAGGAAGAGGGAATCGTGGTGGCAGTGGGCCAGGACTGCTACACGAGAATCTGGAGCCTCCATGATGCCCA
CCTGCTCAGAACCATCCCTTCGCCGTACTCTGCCTCCGAGGACGACATTCCCAGCGTGGCCTTCGCTTCTCGGCTCGGGG
GCATCCGGGGAGCAGCACCAGGGCTGCTCATGGCTGTCCGGCAGGACCTTTATTGTTTCCCTTTCAGCTAA

Alignment

ORF - retro_ptro_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKRLRLLQEEDRRKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERKKVQIRSMDPSALA
          ME..RLRLL.EE...KK.ARMGFNASSMLRKSQLGFLNVT.Y..LA.ELR.SCMERKKVQIRS.DPS.LA
Retrocopy MEAERLRLLEEEAKLKKVARMGFNASSMLRKSQLGFLNVTSYSRLANELRVSCMERKKVQIRSLDPSSLA

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

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

Parental  TNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFHDSAVTSVRILQ
          T.V.TGH.QSF.T.SDVLAQQFA..APLLFNGCRSGEIFAIDLRC.N.GKGW.ATRLFHDSAVTSV.ILQ
Retrocopy TSVATGHQQSFDTSSDVLAQQFANTAPLLFNGCRSGEIFAIDLRCRNRGKGWRATRLFHDSAVTSVQILQ

Parental  DEQYLMASDMAGKIKLWDLRTTKCVRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTRIWSLHDARLLR
          .EQ.LMASDM.GKIKLWDLR.TKCVRQYEGHVNE.AYLPLHVHEEEGI.VAVGQDCYTRIWSLHDA.LLR
Retrocopy EEQCLMASDMTGKIKLWDLRATKCVRQYEGHVNESAYLPLHVHEEEGIVVAVGQDCYTRIWSLHDAHLLR

Parental  TIPSPYAASKADIPSVAFSSRLGGSRG-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_prefrontal_cortex	0.13 RPM	5.72 RPM
SRP007412_cerebellum	0.32 RPM	4.19 RPM
SRP007412_heart	0.12 RPM	1.66 RPM
SRP007412_kidney	0.78 RPM	5.78 RPM
SRP007412_liver	0.10 RPM	4.22 RPM
SRP007412_testis	16.65 RPM	11.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_46 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_46 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_46 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_101
Gorilla gorilla	retro_ggor_2026
Macaca mulatta	retro_mmul_152

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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 ,