RetrogeneDB ID: retro_cjac_103

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:123843646..123844081(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000014473
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007306
• Aliases: None
• Description: None

Sequence

>retro_cjac_103
ATGGCGTTCACGTTCACGGCCTTCTGCTACATGCTAGCGCTGCTGCTCACTGCCACGCTCATCTTCTTCGCCATTTGGCA
CATTATAGCATTTGATAAGCTGAAGACTGATTACAAGAATCCTATAGACCAGTGTAATACCCTGAATCCTCTTGTACTCC
CAGAGTACCTCATCCATGCTTTCTTCTGTGTCATGTTTCTTTGTGCAGCAGAGTGGCTTACGCTGGGTCTCAATATGCCC
CTCTTGGCATATCATATTTGGAGGTATATGAGTAGACCAGTGATGAGTGGACCAGGACTGTATGATCCTACAACCATCAT
GAATGCAGATATTCTAGCATATTGTCAGAAGGAAGGATGGTGTAAATTAGCTTTTTATCTTCTAGCATTTTTTTACTACC
TATACGGCATGATCTATGTTTTGGTGAGCTCTTAG

Alignment

ORF - retro_cjac_103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFTFAAFCYMLALLLTAALIFFAIWHIIAFDELKTDYKNPIDQCNTLNPLVLPEYLIHAFFCVMFLCAA
          MAFTF.AFCYMLALLLTA.LIFFAIWHIIAFD.LKTDYKNPIDQCNTLNPLVLPEYLIHAFFCVMFLCAA
Retrocopy MAFTFTAFCYMLALLLTATLIFFAIWHIIAFDKLKTDYKNPIDQCNTLNPLVLPEYLIHAFFCVMFLCAA

Parental  EWLTLGLNMPLLAYHIWRYMSRPVMSGPGLYDPTTIMNADILAYCQKEGWCKLAFYLLAFFYYLYGMIYV
          EWLTLGLNMPLLAYHIWRYMSRPVMSGPGLYDPTTIMNADILAYCQKEGWCKLAFYLLAFFYYLYGMIYV
Retrocopy EWLTLGLNMPLLAYHIWRYMSRPVMSGPGLYDPTTIMNADILAYCQKEGWCKLAFYLLAFFYYLYGMIYV

Parental  LVSS
          LVSS
Retrocopy LVSS

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	6.81 RPM
SRP051959_heart	0.07 RPM	7.23 RPM
SRP051959_kidney	0.09 RPM	5.70 RPM
SRP051959_liver	0.04 RPM	7.95 RPM
SRP051959_lung	0.05 RPM	6.47 RPM
SRP051959_lymph_node	0.07 RPM	6.44 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.80 RPM
SRP051959_spleen	0.11 RPM	6.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_103 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031178	2 retrocopies	retro_cfam_658, retro_cfam_697,
Callithrix jacchus	ENSCJAG00000007306	1 retrocopy	retro_cjac_103 ,
Callithrix jacchus	ENSCJAG00000008013	1 retrocopy	retro_cjac_2474,
Equus caballus	ENSECAG00000026814	1 retrocopy	retro_ecab_685,
Loxodonta africana	ENSLAFG00000014841	1 retrocopy	retro_lafr_963,
Nomascus leucogenys	ENSNLEG00000012704	1 retrocopy	retro_nleu_1896,
Otolemur garnettii	ENSOGAG00000024582	1 retrocopy	retro_ogar_2271,
Ochotona princeps	ENSOPRG00000005287	4 retrocopies	retro_opri_198, retro_opri_269, retro_opri_366, retro_opri_894,
Tupaia belangeri	ENSTBEG00000010265	3 retrocopies	retro_tbel_2080, retro_tbel_3728, retro_tbel_572,
Tarsius syrichta	ENSTSYG00000011295	1 retrocopy	retro_tsyr_1540,
Tursiops truncatus	ENSTTRG00000008259	1 retrocopy	retro_ttru_261,