RetrogeneDB ID: retro_cjac_1139

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:38810066..38810663(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBR1
• Ensembl ID: ENSCJAG00000038083
• Aliases: None
• Description: carbonyl reductase 1 [Source:HGNC Symbol;Acc:1548]

Sequence

>retro_cjac_1139
GAGTACGGAGGCCTGGACATGCTGGTCAACAACGCGGGCATCGCCTTCAAGGTTGCTGATCCCATACCCTTTCATATTCA
AGCTGAAGTGACGATGAAGACAAACTTCTTTGGTACTTGAGATGTCTGCACAGAGTTACTCCCTCTAATAAAACCCCAAG
GGAGAGTGGTGAATGTATCTAGCACCGTGAGTCTCAGGGCCCTAAAAAGCTGCAGCCCTGAGCTGAAGCAGAAGTTCCTC
AGTGAGACCGTCATCACTGAGGAGGAGCTGGTGGGGCTCATGAATAAGTTCGTGGAGGATACAAAGAAGGGAGTGCACCA
GAAGGCGGGCTGGCCCAACACCGCATACGGGGTGATGAAGGTCGGCGTCACCATGCTGTCCAGGATCCACGCCAGGAAAC
TGAGCGAGCAGAGGAAAGTGCACAAGATCCTCCTGAATGTCTGCTGCCCAGGGTGGGTGAGAACGGACATGGCGTGACCC
AATGCCACCAAGAGCCCGGAAGAAGGAGCAGAGACCCCTGTGTACTTGGCCCTTTTGACCCCGGATGCGGAGGGGCCCCA
TGGACAGTTTGTTTCAGAGAAGAAAGTTGAACAGTGG

Alignment

ORF - retro_cjac_1139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 71.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYGGLDVLVNNAGIAFKVADPTPFHIQAEVTMKTNFFGTRDVCTELLPLIKPHGRVVNVSSTVSLRALKS
          EYGGLD.LVNNAGIAFKVADP.PFHIQAEVTMKTNFFGT.DVCTELLPLIKP.GRVVNVSSTVSLRALKS
Retrocopy EYGGLDMLVNNAGIAFKVADPIPFHIQAEVTMKTNFFGT*DVCTELLPLIKPQGRVVNVSSTVSLRALKS

Parental  CSPELQQKFRSET-ITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGVSKIGVTVLSRIQARKLNEQRKG
          CSPEL.QKF.SET.ITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGV.K.GVT.LSRI.ARKL.EQRK.
Retrocopy CSPELKQKFLSETVITEEELVGLMNKFVEDTKKGVHQKAGWPNTAYGVMKVGVTMLSRIHARKLSEQRKV

Parental  DKILLNACCPGWVRTDMAGPNATKSPEEGAETPVYLALLPPDAEGPHGQFVSEKKVEQW
          .KILLN.CCPGWVRTDMA.PNATKSPEEGAETPVYLALL.PDAEGPHGQFVSEKKVEQW
Retrocopy HKILLNVCCPGWVRTDMA*PNATKSPEEGAETPVYLALLTPDAEGPHGQFVSEKKVEQW

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	0.49 RPM	34.46 RPM
SRP051959_heart	1.32 RPM	4.49 RPM
SRP051959_kidney	0.62 RPM	20.41 RPM
SRP051959_liver	0.45 RPM	125.20 RPM
SRP051959_lung	1.25 RPM	6.04 RPM
SRP051959_lymph_node	1.42 RPM	3.20 RPM
SRP051959_skeletal_muscle	0.61 RPM	6.27 RPM
SRP051959_spleen	1.43 RPM	6.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1139 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1139 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1139 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000038083	1 retrocopy	retro_cjac_1139 ,
Monodelphis domestica	ENSMODG00000021047	1 retrocopy	retro_mdom_278,