RetrogeneDB ID: retro_cjac_1184

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:8205602..8206052(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPZB
• Ensembl ID: ENSCJAG00000006715
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, beta [Source:HGNC Symbol;Acc:1491]

Sequence

>retro_cjac_1184
ATGAGTGGTCAGCAGTTGGACTATGCCTTGGACCTAATGAGGCACCTGCCTCTTCAGCAAATTGAGATAAAGTTCAGTGA
CCTGACTGACCTGGTCTCCCGTCTAAGTGAAGACCTCCTGTCTTCAGTTTACCAGATACTGAAAATTGCCAGAGGCAAGG
AGGTGTAAAACCCTTACATTTTGTATGACTACAATAGAGATAGGGATTGCTATATGTCACCATGACATAATAAATATGTC
CCTCCCTTGGAGGATGGGGCCATGCCATTTGCTCAGCTGAGAAAGCTTGAGATGGAAGCAAAGAATGCCTCTGACCAGCA
TCAAGAACTATATTTTGAAGGCAGCATCTCATCTCGTCTGCCTCTAGGATCTGGATCATGGCTTTGCTGAAGTGATCCTC
ATAAATAAAGCTGGAAGGGATCAAAGAAGATCAAAGTTTGCTGGGATTCA

Alignment

ORF - retro_cjac_1184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDS
          MS.QQLD.ALDLMR.LP.QQIE...SDL.DLV..L.EDLLSSV.Q.LKIAR.K.V...Y.L.DYNRD.D.
Retrocopy MSGQQLDYALDLMRHLPLQQIEIKFSDLTDLVSRLSEDLLSSVYQILKIARGKEV*NPYILYDYNRDRDC

Parental  YRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSS-VYLWDLDHGFAGVILIKKAG-
          Y.SP..NKY.PPLEDGAMP.A.LRKLE.EA.NA.DQ...LYFEG..SS.V.L.DLDHGFA.VILI.KAG.
Retrocopy YMSP*HNKYVPPLEDGAMPFAQLRKLEMEAKNASDQHQELYFEGSISS>VCL*DLDHGFAEVILINKAG<

Parental  DGSKKIKGCWDS
          .GSKKIK.CWDS
Retrocopy KGSKKIKVCWDS

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	26.09 RPM
SRP051959_heart	0.00 RPM	26.06 RPM
SRP051959_kidney	0.00 RPM	16.77 RPM
SRP051959_liver	0.00 RPM	12.80 RPM
SRP051959_lung	0.00 RPM	27.70 RPM
SRP051959_lymph_node	0.00 RPM	27.53 RPM
SRP051959_skeletal_muscle	0.00 RPM	36.78 RPM
SRP051959_spleen	0.00 RPM	24.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1184 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006715	1 retrocopy	retro_cjac_1184 ,
Dasypus novemcinctus	ENSDNOG00000018644	3 retrocopies	retro_dnov_1168, retro_dnov_1719, retro_dnov_2663,
Macropus eugenii	ENSMEUG00000002018	1 retrocopy	retro_meug_1958,
Myotis lucifugus	ENSMLUG00000012115	2 retrocopies	retro_mluc_1254, retro_mluc_2204,
Oryctolagus cuniculus	ENSOCUG00000014711	1 retrocopy	retro_ocun_1213,