RetrogeneDB ID: retro_cjac_2059

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 22:9178019..9178562(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSCJAG00000010383
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_cjac_2059
CGGGCTTCCATGCAGCAACAACAGCAGCTAGCCGGTGCCAGAAACAGAAGCCTGGCCCAGCAGATGGAGAATAGACCCTC
TGTCCAGGCAGCATTAAAACTGAAGCAGAGCTGAAAGCGGCGCCTGGGTAAGAGTAACATCCAGGCACGGTTAGGCCGAC
CCACAGGGGCCCTGGCCAGGGGAGCAATCGGAGGACGAGGCCTACCCATAATCCAGAGAGACTTGCCCAGAGGAGGACTA
CGTGGGGGACGTGCCACCAGAACCCTGCTTAGGGGCGGGATGTCGCTCCGAGGTCAAAACCTGCTCCGAGGTGGACGAGC
CGTAGCTCCCCGAATGGGCTTAAGAAGAGGTGGTGTTCGAGGTCGTGGAGGTCCTGGGAGAGGGGGCCTAGGGCGTGGAG
CTGTGGGTCGCGGCAGAATCGGTGGTGGAGGTCGGGGTATGATAGGTCGGGGAAGAGGGGGCTTTGGAGGCCGAGGCCGA
GGCCGTGGACGAGGGAGAGGTGCCCTTGCTCGCCCTGTATTGACCAAGGAGCAGCTGGACAAC

Alignment

ORF - retro_cjac_2059 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 73.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASMQQQQQLASARNRRLAQQMENRPSVQAALKLKQKSLKQRLGKSNIQARLGRPIGALARGAIGGRGLP
          RASMQQQQQLA.ARNR.LAQQMENRPSVQAALKLKQ.S.K.RLGKSNIQARLGRP.GALARGAIGGRGLP
Retrocopy RASMQQQQQLAGARNRSLAQQMENRPSVQAALKLKQ-S*KRRLGKSNIQARLGRPTGALARGAIGGRGLP

Parental  IIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMGRGG
          IIQR.LPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGA.GRG.
Retrocopy IIQRDLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAVGRGR

Parental  IGGRGRGMIGRGKGGFGGRGRGRGRGRGALARPVLTKEQLDN
          IGG.GRGMIGRG.GGF..........RGALARPVLTKEQLDN
Retrocopy IGGGGRGMIGRGRGGFXXXXXXXXXXRGALARPVLTKEQLDN

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	20.21 RPM
SRP051959_heart	0.07 RPM	24.05 RPM
SRP051959_kidney	0.16 RPM	25.45 RPM
SRP051959_liver	0.02 RPM	15.77 RPM
SRP051959_lung	0.08 RPM	29.33 RPM
SRP051959_lymph_node	0.21 RPM	33.93 RPM
SRP051959_skeletal_muscle	0.11 RPM	26.38 RPM
SRP051959_spleen	0.04 RPM	27.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2059 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2059 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2059 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Callithrix jacchus	ENSCJAG00000010383	3 retrocopies	retro_cjac_2059 , retro_cjac_423, retro_cjac_431,
Felis catus	ENSFCAG00000002740	1 retrocopy	retro_fcat_1925,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Mus musculus	ENSMUSG00000001017	2 retrocopies	retro_mmus_1693, retro_mmus_1852,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Ictidomys tridecemlineatus	ENSSTOG00000000660	1 retrocopy	retro_itri_1169,
Tupaia belangeri	ENSTBEG00000012442	1 retrocopy	retro_tbel_293,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,