RetrogeneDB ID: retro_cjac_960

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:28966155..28966442(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC167
• Ensembl ID: ENSCJAG00000005622
• Aliases: None
• Description: coiled-coil domain containing 167 [Source:HGNC Symbol;Acc:21239]

Sequence

>retro_cjac_960
ACAAAAAAGAAGTGGGAGAATCTGGGTGTTGCTCTAGAGATCGATGGGCTAGAGAAGAAGCTGTCCCAGTGTCAGAGAGA
CCTAAAGGCCGTGAACTCCAGGCTCCACAGCGGGGAGCTGAGCCCAGAGGCCAGGAGGTCCCTGGAGAAGGAGAAAACAG
CCTAATGAGCAAAGCCTCCAACTACAAGAAGGAAGTGAAGTTGCTTTGGCAAGAGAACCAGAAGAACATGCTGCTCTCTG
TGGCCATCTTCATCCTTCTGACCCTCGTCTATGCCTACTGGACCATG

Alignment

ORF - retro_cjac_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.63 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TKKKRENLGVALEIDGLEKKLSQCRRDLEAVNSRLHSRELSAEARRSLEKEK-NSLMSKASNYEKELKLL
          TKKK.ENLGVALEIDGLEKKLSQC.RDL.AVNSRLHS.ELS.EARRSLEKEK.NSLMSKASNY.KE.KLL
Retrocopy TKKKWENLGVALEIDGLEKKLSQCQRDLKAVNSRLHSGELSPEARRSLEKEK<NSLMSKASNYKKEVKLL

Parental  RQENWKNMLLSLAIFILLTLIYAYWTM
          .QEN.KNMLLS.AIFILLTL.YAYWTM
Retrocopy WQENQKNMLLSVAIFILLTLVYAYWTM

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	1.15 RPM
SRP051959_heart	0.00 RPM	0.60 RPM
SRP051959_kidney	0.00 RPM	0.51 RPM
SRP051959_liver	0.00 RPM	0.67 RPM
SRP051959_lung	0.00 RPM	0.63 RPM
SRP051959_lymph_node	0.02 RPM	1.12 RPM
SRP051959_skeletal_muscle	0.15 RPM	0.31 RPM
SRP051959_spleen	0.02 RPM	1.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_960 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012069	2 retrocopies	retro_btau_30, retro_btau_517,
Canis familiaris	ENSCAFG00000030835	1 retrocopy	retro_cfam_1854,
Callithrix jacchus	ENSCJAG00000005622	2 retrocopies	retro_cjac_3293, retro_cjac_960 ,
Felis catus	ENSFCAG00000006745	1 retrocopy	retro_fcat_1558,
Mus musculus	ENSMUSG00000024018	1 retrocopy	retro_mmus_3487,
Otolemur garnettii	ENSOGAG00000000921	1 retrocopy	retro_ogar_880,
Pongo abelii	ENSPPYG00000016563	1 retrocopy	retro_pabe_2092,