RetrogeneDB ID: retro_cjac_2996

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:83670739..83672218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DUS2L
• Ensembl ID: ENSCJAG00000015797
• Aliases: None
• Description: None

Sequence

>retro_cjac_2996
ATGATTGTGAATACCCTCTCTCTGTGCTACCATAACAAGCTAATTCTGGCCCCAGTGGTTCGGGTAGGGACTCTTCCAAT
GCGGCTGCTCGCCCTGGATTATGGAGCGGACATTGTTTACTGTGAGGAGCTGATCGACCTCAAGATGATTCAGTGCAAGA
GAGTTGTCAATGAGGTGCTTAGCACAGTGGACTTTGTTGCTCCTGATGATCGAGTTGTCTTCCGCACCTGTGAAAGAGAG
CAGAACAGGGTTGTCTTCCAGATGGGGACTTCAGACGCAGAGCGAGCCCTTGCTGTGGCCAGGCTTGTAGAAAATGATGT
GGCTGGTATTGATGTCAACATGGGCTGTCCAAAAGAATATTCCACCAAAGGAGGAATGGAAGCTGCTCTGTTGTCAGACC
CTGACAAGATTGAGAAGATCCTCAGCACTCTTGTTAAAGGGACACGCCAACCTGTGACCTGCAAGGTTCGCATCCTGCCA
TCGCTAGAAGATACCCGGAGCCTTGTGAAGCGGATAGAGAGGACTGGCATTGCTACCATTGTGGTTCCTGGGAGGAAGCA
GGAGGAGCGACCTCAGCATCCTGTCAGCTGTGAGGTCATCAAAGCCATTGCTGATACCCTCTCCATTCCTGTCATAGCCA
ATAGAGGATCTCATGACCACATCCAAAGGTATTCGGACGTAGAGGACTTTCGACAAGCCACGGCAGCCTCTTCCGTGATG
GTGGCTTGAGCTGCCATGTGGAACCCATCTATCTTTCTCAAGGAGGGTCTGCGGCCCCTGGAGGAGGTCATGCAGAAATA
CAACAGATACGCGGTGTAGTATGACAACCACTATACCAACACTAAGTACTGCTTGTGCCAGATGCTATGAGAACAGTTGG
ATTCTCCCCAGGGAAGGTTGCTCCATGCTGCCCAGTCTTCCCAGGAAATTTGTGAGGCCTTTGGCCTTGGTGCCTTCTAT
GAGGAGACCACACAGGAGCTGGATGCCCAGCGGGCCAAGCTCTCAGCCAGGACTTCAGAGTAGACCGGGGAGCCAGCTGA
AGATACCTCTGGTGTGATTAAGATGGCTGTCAAGTTTGACCGGAGGGCATATTCAGCCCAGATCACCCCCAAGATGTGTC
TGCTAGAGTGGTGCCAGAGAGAGAAGTTGCCACAGCCCATGTATGAAATGGTTCAACGCCCTATAGACTGCCTGTTCTCT
TCTATTGTCACCATTGCTGAACAAAACTATCAGTCTACCTTGTGGGACAAGTCCAAGAAACTGGCGGAGCAGGCTGCGGC
CATCATATGTCTGTGGAGCCAGGGCCTCCCTGAGGGTCAGCTGGGTGAGGAGAACCCTTCCTTGCACAAGCAAAAGAGGG
AGGCTCCTGACCATGACTGTGGGGGCTCCAGAGCTCAGGAGCTAGCATAACCTGGGGAGCTGTGCAAGAAGCCCTTTGTG
GCCTTGGGAAGCAGTGAAGAGAGCCCCCTGGAAGGCTGG

Alignment

ORF - retro_cjac_2996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIVNSLSLCYHNKLILAPMVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDD
          MIVN.LSLCYHNKLILAP.VRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDD
Retrocopy MIVNTLSLCYHNKLILAPVVRVGTLPMRLLALDYGADIVYCEELIDLKMIQCKRVVNEVLSTVDFVAPDD

Parental  RVVFRTCEREQNRVVFQMGTSDAERALAVARLVENDVAGIDVNMGCPKEYSTKGGMGAALLSDPDKIEKI
          RVVFRTCEREQNRVVFQMGTSDAERALAVARLVENDVAGIDVNMGCPKEYSTKGGM.AALLSDPDKIEKI
Retrocopy RVVFRTCEREQNRVVFQMGTSDAERALAVARLVENDVAGIDVNMGCPKEYSTKGGMEAALLSDPDKIEKI

Parental  LSTLVKGTHRPVTCKIRILPSLEDTLSLVKRIERTGIAAIAVHGRKREERPQHPVSCEVIKAIADTLSIP
          LSTLVKGT..PVTCK.RILPSLEDT.SLVKRIERTGIA.I.V.GRK.EERPQHPVSCEVIKAIADTLSIP
Retrocopy LSTLVKGTRQPVTCKVRILPSLEDTRSLVKRIERTGIATIVVPGRKQEERPQHPVSCEVIKAIADTLSIP

Parental  VIANGGSHDHIQRYSDIEDFRQATAASSVMVARAAMWNPSIFLKEGLRPLEEVMQKYIRYAVQYDNHYTN
          VIAN.GSHDHIQRYSD.EDFRQATAASSVMVA.AAMWNPSIFLKEGLRPLEEVMQKY.RYAV.YDNHYTN
Retrocopy VIANRGSHDHIQRYSDVEDFRQATAASSVMVA*AAMWNPSIFLKEGLRPLEEVMQKYNRYAV*YDNHYTN

Parental  TKYCLCQMLREQLESPQGRLLHAAQSSREICEAFGLGAFYEETTQELDAQRAKLSARTSEETGEPAEDTS
          TKYCLCQML.EQL.SPQGRLLHAAQSS.EICEAFGLGAFYEETTQELDAQRAKLSARTSE.TGEPAEDTS
Retrocopy TKYCLCQML*EQLDSPQGRLLHAAQSSQEICEAFGLGAFYEETTQELDAQRAKLSARTSE*TGEPAEDTS

Parental  GVIKMAVKFDRRAYSAQITPKMCLLEWCRREKLPQPMYETVQRPIDRLFSSIVTVAEQKYQSTLWDKSKK
          GVIKMAVKFDRRAYSAQITPKMCLLEWC.REKLPQPMYE.VQRPID.LFSSIVT.AEQ.YQSTLWDKSKK
Retrocopy GVIKMAVKFDRRAYSAQITPKMCLLEWCQREKLPQPMYEMVQRPIDCLFSSIVTIAEQNYQSTLWDKSKK

Parental  LAEQAAAIVCLRSQGLPEGRLGEENPFLHKRKREAPDQDCGGSRAQELAQPGELCKKPFVALGSGEESLL
          LAEQAAAI.CL.SQGLPEG.LGEENP.LHK.KREAPD.DCGGSRAQELA.PGELCKKPFVALGS.EES.L
Retrocopy LAEQAAAIICLWSQGLPEGQLGEENPSLHKQKREAPDHDCGGSRAQELA*PGELCKKPFVALGSSEESPL

Parental  EGW
          EGW
Retrocopy EGW

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
SRP051959_colon	0.00 RPM	3.08 RPM
SRP051959_heart	0.05 RPM	3.24 RPM
SRP051959_kidney	0.16 RPM	3.55 RPM
SRP051959_liver	0.02 RPM	3.64 RPM
SRP051959_lung	0.16 RPM	6.30 RPM
SRP051959_lymph_node	0.05 RPM	12.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.84 RPM
SRP051959_spleen	0.00 RPM	7.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2996 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2996 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015797	1 retrocopy	retro_cjac_2996 ,