RetrogeneDB ID: retro_cjac_789

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:64135999..64137067(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATF2
• Ensembl ID: ENSCJAG00000008085
• Aliases: None
• Description: None

Sequence

>retro_cjac_789
GAAGTACCACTGGCACAAACTGCACAGCCCACATCAGCTATTGTTCGTCCAGCATCATTACAGGTTCCCAATGTGCTGCT
AACAAGTTCTGACTCAAGTGTCATTATTCAGCAGGCAGTACCTTCACCAACCTCAAGTACTGTAATCACCCAGGCACCAT
CCTCTAACAGGCCAATTGTCCCTGTACCGGGCCCATTTCCTCTTCTGTTACATCTTCCTAATGGACAAGCCATGCCTGTT
GCTATTCCTGCATCAATTACAAGTTCTAATGTGCATGTTTCAGCTGCAGTCCCACTCGTTCCACCAGTCACCATGGTGCC
TAGTGTTCAGGAAATCCCAGGTCCTTCGTCTCCCCAACCAGTACAGTCAGAAGCAAAAATGAGATTAAAAGCTGCTTTGA
CCCAGCAACATCCTCCAGTTACCAATGGTGATACTGTCAAAGGTCATGGTAGTGGACTGGTTAGGACTCAGTCAGAGGAA
TCTTGACCACAGTCATTACAACAGCCAGCCACATCCACTACAGAAACTCTGGCTTCTCCAGCTCACACAACTCCATAGAC
CCAAAGTACAAGTGGTCATCTGAGAAGAGCAGCTAATGAAGATCCTGATGAAAAAAAGAGAAAGTTCTTAGAGCAAAATA
GAGCAGCAGCTTCAAGATGCCGACAAAAAAGGAAAGTCTGGGTTCAGTCTTTACAGAAGAAAGCAGAAGACTTGAGTTCA
TTAAATGGTCAACTGCAGAGTGAAGTCACCCTGCTGAGAAATGAAGTGGCACAGCTGAAACAGCTTCTTTTGGCTCATAA
AGATTAGCCTGTAACTGCCATGCAGAAGAAATGTGGCTATCATACTGCTGTAAAAGATCATAGTTCAGAAGACATTTCAG
TGCCGAGCAGTCCACATACAGAAGCTATACAACATAGTTCGGTCAGCACATCCAGTGGAGTCAGTTCAACCTCCAAGGCA
GAAGCTGTAGCCACTTCAGTCCTCACCCAGATGGCGGACAAGAGTACAGAGCCTGCTCTTTCACAGATCGTTACGGCTCC
TTCCTCCCAGTCACAGCCCTCCGGAAGT

Alignment

ORF - retro_cjac_789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 73.1 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVPLAQTAQPTSAIVRPASLQVPNVLLTSSDSSVIIQQAVPSPTSSTVITQAPSSNRPIVPVPGPFPLLL
          EVPLAQTAQPTSAIVRPASLQVPNVLLTSSDSSVIIQQAVPSPTSSTVITQAPSSNRPIVPVPGPFPLLL
Retrocopy EVPLAQTAQPTSAIVRPASLQVPNVLLTSSDSSVIIQQAVPSPTSSTVITQAPSSNRPIVPVPGPFPLLL

Parental  HLPNGQTMPVAIPASITSSNVHVPAAVPLVRPVTMVPSVPGIPGPSSPQPVQSEAKMRLKAALTQQHPPV
          HLPNGQ.MPVAIPASITSSNVHV.AAVPLV.PVTMVPSV..IPGPSSPQPVQSEAKMRLKAALTQQHPPV
Retrocopy HLPNGQAMPVAIPASITSSNVHVSAAVPLVPPVTMVPSVQEIPGPSSPQPVQSEAKMRLKAALTQQHPPV

Parental  TNGDTVKGHGSGLVRTQSEESRPQSLQQPATSTTETPASPAHTTPQTQSTSGRRRRAANEDPDEKRRKFL
          TNGDTVKGHGSGLVRTQSEES.PQSLQQPATSTTET.ASPAHTTP.TQSTSG..RRAANEDPDEK.RKFL
Retrocopy TNGDTVKGHGSGLVRTQSEES*PQSLQQPATSTTETLASPAHTTP*TQSTSGHLRRAANEDPDEKKRKFL

Parental  ERNRAAASRCRQKRKVWVQSLEKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLAHKDCPVTAMQKKSGY
          E.NRAAASRCRQKRKVWVQSL.KKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLAHKD.PVTAMQKK.GY
Retrocopy EQNRAAASRCRQKRKVWVQSLQKKAEDLSSLNGQLQSEVTLLRNEVAQLKQLLLAHKD*PVTAMQKKCGY

Parental  HTADKDDSSEDISVPSSPHTEAIQHSSVSTSNGVSSTSKAEAVATSVLTQMADQSTEPALSQIVMAPSSQ
          HTA.KD.SSEDISVPSSPHTEAIQHSSVSTS.GVSSTSKAEAVATSVLTQMAD.STEPALSQIV.APSSQ
Retrocopy HTAVKDHSSEDISVPSSPHTEAIQHSSVSTSSGVSSTSKAEAVATSVLTQMADKSTEPALSQIVTAPSSQ

Parental  SQPSGS
          SQPSGS
Retrocopy SQPSGS

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	0.78 RPM	23.96 RPM
SRP051959_heart	0.86 RPM	31.70 RPM
SRP051959_kidney	0.95 RPM	32.92 RPM
SRP051959_liver	1.00 RPM	28.03 RPM
SRP051959_lung	0.89 RPM	39.32 RPM
SRP051959_lymph_node	0.66 RPM	38.54 RPM
SRP051959_skeletal_muscle	0.48 RPM	23.50 RPM
SRP051959_spleen	0.74 RPM	42.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_789 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_789 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	ENSCJAG00000008085	1 retrocopy	retro_cjac_789 ,
Otolemur garnettii	ENSOGAG00000011373	1 retrocopy	retro_ogar_769,