RetrogeneDB ID: retro_cjac_3028

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:132608004..132608626(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHARPIN
• Ensembl ID: ENSCJAG00000021452
• Aliases: None
• Description: SHANK-associated RH domain interactor [Source:HGNC Symbol;Acc:25321]

Sequence

>retro_cjac_3028
GCCCGGGCCATTGCAGGTGGGGACAAGAAGGGGGCAGTCCAAGCAGCAGCCGTCCTGGCCCAGCATCGTGAGGCCCTCAG
TGTTCAGCTTCAGGAGGCCTGCTTCCCACCTGGCCCCATCAGACTGCAGGTCACACTTGAAGATGCTGCTTCTGCTGCAT
CCACCGCATCCTCTGCCCACATCACACTGCAGGTCCACGCCCACTGCACCATTGCAGATCTCCAGGAGCAGTGTTATCAG
AGCTTGTTTTCCCACCGGCCGTGCAACGCTGGGTCATTGGGCAGTGCTTGTGTGTGCCTGAGCTCAGTCTTGCCTCCTAT
GGGGTTTGGCAGGATGAGGACCCTGCTTTCCTCTACTTGCTGACAGCTCTTCGAAAAGCCCCAGCCACAGGACCCAGCCC
TCATTGCCCCGAGAAGACGGATGGGGAACTTGGACGCTTGTTTCCCGCATCATTGGGCCAGCTCCCAGGCCCCCAGCCAG
CCACTTCCAGCCTGCCCAGTCCTCTCCAGCCCGGCTGGCCCTGTCCTTCCTGCACCTTCATCAATGCCCAAGCCACCCTG
GCTGTCAGATGTGTAGCACCCAGAGGCCCTGCACTTGGGACCCCCTTGCCACAGCTTCCACC

Alignment

ORF - retro_cjac_3028 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.05 %
• Parental protein coverage: 53.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARAIAGGDEKGAAQAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHIALQVHPHCT
          ARAIAGGD.KGA.QAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHI.LQVH.HCT
Retrocopy ARAIAGGDKKGAVQAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHITLQVHAHCT

Parental  IAALQEQ-VFSELGFPPAVQRWVIGQCLCVPERSLASYGVRQDGDPAFLYLLTAPQEAPAIGPSPHRPQK
          IA.LQEQ.V.SEL.FPPAVQRWVIGQCLCVPE.SLASYGV.QD.DPAFLYLLTA...APA.GPSPH.P.K
Retrocopy IADLQEQ<VLSELVFPPAVQRWVIGQCLCVPELSLASYGVWQDEDPAFLYLLTALRKAPATGPSPHCPEK

Parental  TDGELGRLFPASLGLPPGPQPATSSLPSPLQPGWPCPSCTFINA-PSRPGCEMCSTQRPCTWDPLAAAST
          TDGELGRLFPASLG..PGPQPATSSLPSPLQPGWPCPSCTFINA.PS.PGC.MCSTQRPCTWDPLA.AST
Retrocopy TDGELGRLFPASLGQLPGPQPATSSLPSPLQPGWPCPSCTFINA<PSHPGCQMCSTQRPCTWDPLATAST

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	2.86 RPM
SRP051959_heart	0.00 RPM	5.89 RPM
SRP051959_kidney	0.02 RPM	6.68 RPM
SRP051959_liver	0.00 RPM	4.96 RPM
SRP051959_lung	0.00 RPM	5.12 RPM
SRP051959_lymph_node	0.00 RPM	4.70 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.94 RPM
SRP051959_spleen	0.00 RPM	4.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3028 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3028 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3028 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	ENSCJAG00000021452	1 retrocopy	retro_cjac_3028 ,