RetrogeneDB ID: retro_cjac_1007

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:119319458..119320727(+)
• Located in intron of: ENSCJAG00000014418

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000013514
• Aliases: None
• Description: None

Sequence

>retro_cjac_1007
AGGACCGGGCAGTTAAATGGCACCTGCACCAGCTCAGTGGACATGGAGCTCTTCCTCCATTACTCCCTCATCCCATCACT
CTTCATCATTTTGATCTTGTCCTTCCTCCAAAGACGAGAGCATCGTAGACAGAGAGATGATACCTCTTACCTTCTGGGGA
ACCGCTTTGGAATCATCATACCTCTGGACTTTGTGGGCACTTTCAGTAACCGATGGTCCTATGGAATCGCCTTTGGGGCC
ACAGCTAATAAGGTCATGTTTTTGTTCTCAGAAGGCTACCAGCCCCTGCAGATCCCGCAGTGGGCCCAAGCCTTTGAGCT
TATGATTGGAGGCCTTGAAGTTGGCCTGTCTCACTTCCCCTTCTTTGTGTGCCTCTCGTCAGAGTTCCAGCTGGTCAGCT
CCACCCTGGGCTTCTGCTACTCTCTTATCTGGTTTGCTGTCACCATTCTTCAAGTTTCACAGTGTCCCCATGGGCAGTTC
GTGGGGAAGTACGAGACCCTTGTGTTCTACTGGCCCTCACTGCTGTGCCTCGCCTTCCTGCTGGGCCGCTTCCTGTATAT
GTTTGTCAAGGCTCTGAGGGTACACCTTGGCTGGGAGCTCCAGGTGGAAGAAAAGCCTGTCCTGGAAGCGCACCAGGCAG
AGCACGTCAAGCAGCTCCTGAGGACACCCCACTCACAAGAAGAAAAAAAGTCTTGGTTCCAAACCAGGATATATGAGTGG
GATCCCTGCTTTCAATTCCCAAGCAGAATGATTGGAACCATTGTATTGGCTTTCATCTGCCTGTACCTTTTCATTGTCAT
CGAGTTCAGCATGTTTGTGTACGTGAGAGATGAGCTGGACATGTTTGAAAACAAGCTGGAGAGCTACATCAACTCCGTGA
ACCATTCAGGGATCCTGACCCCAGGTATCCTGCAGGTGAAAGAGCTGATCAGCGTTACCAAAGGAGTCTGGGTGGCGACC
ATTTTACCTGCCTCACTCACGTGTGTGAGCTATCTGTTCCACATTTTGGTCTGTTACAGAAAGCACATAAAGAGGCTCTG
GGCAGGAGATAAACACTTTCTGCCTTTGAGGTTTCATAACCCGGCCTCGTCGGAGAGCGTGGTGGCCATTGCAAGGTACT
CTGGCTGGCAAATAGCCTATATTCTATGGGGCTACCTCATCATTCACGTGGTGCAGAGCCTATGTGGCATGGCAATCATG
TACGGTCTGGTGCTGCCCATCATCCACAAACAGGGCCTAGAGATGCTGCGAGGGCTGGGCATCGGGATG

Alignment

ORF - retro_cjac_1007 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.35 %
• Parental protein coverage: 68.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGIIMPLDFVGTFSN
          RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGII.PLDFVGTFSN
Retrocopy RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGIIIPLDFVGTFSN

Parental  RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFELLIGGLEVGLSHFPFFACLSSEFQLVSSTLGFCY
          RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFEL.IGGLEVGLSHFPFF.CLSSEFQLVSSTLGFCY
Retrocopy RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFELMIGGLEVGLSHFPFFVCLSSEFQLVSSTLGFCY

Parental  SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA
          SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA
Retrocopy SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA

Parental  HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEFCMFVYVRDELD
          HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEF.MFVYVRDELD
Retrocopy HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEFSMFVYVRDELD

Parental  MFENKLESYITSVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD
          MFENKLESYI.SVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD
Retrocopy MFENKLESYINSVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD

Parental  KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPIVHKQGLEMLRGLG
          KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPI.HKQGLEMLRGLG
Retrocopy KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPIIHKQGLEMLRGLG

Parental  IGI
          IG.
Retrocopy IGM

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	0.02 RPM	1.62 RPM
SRP051959_heart	0.00 RPM	1.05 RPM
SRP051959_kidney	0.95 RPM	28.93 RPM
SRP051959_liver	3.79 RPM	87.57 RPM
SRP051959_lung	0.26 RPM	5.17 RPM
SRP051959_lymph_node	0.07 RPM	5.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.13 RPM
SRP051959_spleen	0.04 RPM	0.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1007 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1007 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1007 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	ENSCJAG00000013514	1 retrocopy	retro_cjac_1007 ,