RetrogeneDB ID: retro_cjac_1181

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:4776286..4777281(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010707
• Aliases: None
• Description: None

Sequence

>retro_cjac_1181
GGCCTGGCTGCCATGGACACCAAGCTGGAGGTGGCGGTGCTGCAGGAAAGCGTCGCAAAGATGGGCATCGCATCCAGGGC
TGAGATTGAGGACTGGTTCATGTCAGAGATCCTGGGATTGTCTGGCACCATGGATCTGCTGGACTGGAGCAGCCTCATCG
ACAGCAGGACCAAGCTCTCCAAGCACCTGGTGGTCCCTACCACACAGACCGATAGCTGGAGCCCCTGCTGTCCCAGTTTA
CTAAGGAGGAGGAGCTGCAGATGACGAGGATGCTGCAGCGGATGGACGTCCTGGCCAAGAAAGCGACAGAGGTGGGTGTG
CGGCTGATGGTGGAGGCTGAGCAGACCTACTTCCAGCCAGCCATCAGCTGCCTGACGCTAGAGATGCAGCGCAGATTCAA
CGTAGAGAGGCCACTCATCTTCAGCACGCACCAGTGCTACCTCAAGGATTCCTATGACAATGTGACCCTGGATGTGGAGC
TGGCTCGCCGTGAGGGCTGGTGTTTTGGTTCCACCCTGGTGTGGGGCGCATACATGGCCCAGGAGCGAGCCCGTGAGGCA
GAGATCGGCTATGAGGACCCCATGAACCCCACGTACAAGGCCACCAATGCCATGTACCACAGGTGTCTGGACCACGTGTT
GGAGGAGCTGAAGCACAATGCCAAGGCCAAGGTGATGGTGGCCACCCACAACGAGGACCCAGTGCGCTTCAGGCTGCCCA
GGATGGAGGAGCTGTGCCTGCATCCCGCTGGCCACCAGGTGTATTTTGGCCAGCTGCTAGGCATGTGTGACCAGATCAGT
TTCCTGCTGGGCCAGGCAGGCTACCCCGTGTACAAGTATGTGCCCTAGGGTCTGGTGATGGACGTGCTGCCCTACCTGTC
CCGCCGGGCCCTGGAGAACAGCAGCGTCATGAAGGACGCCCATCAGGAGCGGGAGCTGCTGTGGCTGGTGCTCTTGTGGC
GGCTCCGAACTGGCAGCTTCTTCCATCGCCCTGCC

Alignment

ORF - retro_cjac_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 56.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GHATRPSHLQIKILEESIAKMGITSRAEIEDWFTAETLGVSGTVDLLDWSSLIDSRTKLCKHLVVPNTQT
          G.A.....L....L.ES.AKMGI.SRAEIEDWF..E.LG.SGT.DLLDWSSLIDSRTKL.KHLVVP.TQT
Retrocopy GLAAMDTKLEVAVLQESVAKMGIASRAEIEDWFMSEILGLSGTMDLLDWSSLIDSRTKLSKHLVVPTTQT

Parental  GQ-LEPLLSRFTEEEELQMTRMLQRMDVLAKKATEVGVRLMVDAEQTYFQPAISRLTLEMQRRFNVERPL
          ...LEPLLS.FT.EEELQMTRMLQRMDVLAKKATEVGVRLMV.AEQTYFQPAIS.LTLEMQRRFNVERPL
Retrocopy DS<LEPLLSQFTKEEELQMTRMLQRMDVLAKKATEVGVRLMVEAEQTYFQPAISCLTLEMQRRFNVERPL

Parental  IFSTHQCYLKDAYDNVTLDVELARREGWCFGSKLVRGAYMAQERARSAEIGYQDPINPTYEATNAMYHRC
          IFSTHQCYLKD.YDNVTLDVELARREGWCFGS.LV.GAYMAQERAR.AEIGY.DP.NPTY.ATNAMYHRC
Retrocopy IFSTHQCYLKDSYDNVTLDVELARREGWCFGSTLVWGAYMAQERAREAEIGYEDPMNPTYKATNAMYHRC

Parental  LDHVLEEVKHNARAKVMVATHNEDSVRFTLRRMEELCLHPAGHQVYFGQLLGMCDQISLPLGQAGYPVYR
          LDHVLEE.KHNA.AKVMVATHNED.VRF.L.RMEELCLHPAGHQVYFGQLLGMCDQIS..LGQAGYPVY.
Retrocopy LDHVLEELKHNAKAKVMVATHNEDPVRFRLPRMEELCLHPAGHQVYFGQLLGMCDQISFLLGQAGYPVYK

Parental  YVPYGPVMDVLPYLSRLALENSS-LKGARRERQLLWLELLRRLQTGSFFHRPA
          YVP.G.VMDVLPYLSR.ALENSS..K.A..ER.LLWL.LL.RL.TGSFFHRPA
Retrocopy YVP*GLVMDVLPYLSRRALENSSVMKDAHQERELLWLVLLWRLRTGSFFHRPA

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	0.91 RPM
SRP051959_heart	0.00 RPM	6.95 RPM
SRP051959_kidney	0.00 RPM	2.95 RPM
SRP051959_liver	0.04 RPM	9.83 RPM
SRP051959_lung	0.00 RPM	3.86 RPM
SRP051959_lymph_node	0.00 RPM	0.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.92 RPM
SRP051959_spleen	0.00 RPM	1.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1181 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1181 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	ENSCJAG00000010707	1 retrocopy	retro_cjac_1181 ,