RetrogeneDB ID: retro_cjac_3890

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285903.1:359707..360069(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TEN1
• Ensembl ID: ENSCJAG00000013878
• Aliases: None
• Description: TEN1 CST complex subunit [Source:HGNC Symbol;Acc:37242]

Sequence

>retro_cjac_3890
ATGCTGCCCAAACTTGGGACCCATTCCTTCCCCTGGAAAGTCAATACAAGCCAAGTTCCTGGTGGGAGCACACTGAGAAC
ATTTGGCAGGTTGTGCCTCTATGATATCGTCAGGCTAGAGTGACGCTGATGGCTCGGCATGGATCTGGTCCACACCAGGT
TGTTTGTACCAAGTTGGTGAAGCCCTTTCAAGCCCATGTGGGCTCCATGTACATCGTCCTCGGGGAGCTCCAGCTCCAGC
AAGCTGGAGACTCCCTGGTAAACGCACTGGAGCTGAACTGTGTGGAGGGGATGGACCTGCCCTTGTGAGAACAAGCCAAG
CAGGAGCAGAGGCAGTACCAGTGGGAGAGGGATGGCAGCCAG

Alignment

ORF - retro_cjac_3890 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLPKPGIFYLPWEISAGQVPDGSTLRTFGRLCLYDMI-QSRVTLTAQHGSNQHQVLVCTKLVEPFHAQVG
          MLPK.G....PW.....QVP.GSTLRTFGRLCLYD...Q.RVTL.A.HGS..HQV.VCTKLV.PF.A.VG
Retrocopy MLPKLGTHSFPWKVNTSQVPGGSTLRTFGRLCLYDIV<QARVTLMARHGSGPHQV-VCTKLVKPFQAHVG

Parental  SLYIVLGELQHQQDGGSVVKARVLTCVEGMNLPLLEQAIREQRLYQQERGGGQ
          S.YIVLGELQ.QQ.G.S.V.A..L.CVEGM.LPL.EQA..EQR.YQ.ER.G.Q
Retrocopy SMYIVLGELQLQQAGDSLVNALELNCVEGMDLPL*EQAKQEQRQYQWERDGSQ

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	2.04 RPM
SRP051959_heart	0.00 RPM	2.53 RPM
SRP051959_kidney	0.00 RPM	3.39 RPM
SRP051959_liver	0.00 RPM	3.18 RPM
SRP051959_lung	0.00 RPM	2.90 RPM
SRP051959_lymph_node	0.00 RPM	2.03 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.96 RPM
SRP051959_spleen	0.00 RPM	3.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3890 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3890 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3890 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013878	5 retrocopies	retro_cjac_3524, retro_cjac_3525, retro_cjac_3554, retro_cjac_3890 , retro_cjac_582,
Gorilla gorilla	ENSGGOG00000013858	1 retrocopy	retro_ggor_2810,
Macaca mulatta	ENSMMUG00000029820	1 retrocopy	retro_mmul_1164,
Nomascus leucogenys	ENSNLEG00000001980	1 retrocopy	retro_nleu_1795,
Pongo abelii	ENSPPYG00000008646	1 retrocopy	retro_pabe_3425,