RetrogeneDB ID: retro_cjac_932

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:83552905..83553384(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006733
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM195A
• Ensembl ID: ENSCJAG00000011979
• Aliases: None
• Description: family with sequence similarity 195, member A [Source:HGNC Symbol;Acc:14142]

Sequence

>retro_cjac_932
ATGTACACCATCACCAAGGGGCCCAGCAAGCTGGTCGCGCAGCGCCGCACAGGTCCCACGCAGCAGCAGGTGGAGGGCCG
GCTCGGCGAGCTCCTGAAATGCCGGCAGCCCGCGCCGCCGACCGCGCAGCCCCGTGGGCGCAGCCCTTCGCGCAGCCGCC
GGGACCCTGGCCCCTGTCGAGTCCGGGGCCAAGGCTTGTGTTCAATCGTGTGAATGGCCGGCGGGCTCCCTCCACGTCCC
CATCCCTCGAGGGGACCCAGGAGACCTACACACCGGCCCACGAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCAG
GTGCAGCAGCAGCTGAATGGTGGCCCAGCCAGTAAGGGCGGGCCGAGGCCTGTGCAGTACGTGGAGAGGACCCCCAATCC
CCGGCTGCAGAACTTCGTGCCCATTGACCTGGACGAGTGGTGGGCGCAGCAGTTCCTGGCTAGAATCACCAGCTGTTCC

Alignment

ORF - retro_cjac_932 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTAQP-PRAQPFAQPPGPWPLSSPGPRLVFN
          MYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTAQP.P.AQPFAQPPGPWPLSSPGPRLVFN
Retrocopy MYTITKGPSKLVAQRRTGPTQQQVEGRLGELLKCRQPAPPTAQP<PWAQPFAQPPGPWPLSSPGPRLVFN

Parental  RVNGRRAPSTSPSLEGTQETYTLAHEENVRFVSEAWQQVQQQLNGGPAGEGGPRPVQYVERTPNPRLQNF
          RVNGRRAPSTSPSLEGTQETYT.AHEENVRFVSEAWQQVQQQLNGGPA..GGPRPVQYVERTPNPRLQNF
Retrocopy RVNGRRAPSTSPSLEGTQETYTPAHEENVRFVSEAWQQVQQQLNGGPASKGGPRPVQYVERTPNPRLQNF

Parental  VPIDLDEWWAQQFLARITSCS
          VPIDLDEWWAQQFLARITSCS
Retrocopy VPIDLDEWWAQQFLARITSCS

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	0.04 RPM	1.44 RPM
SRP051959_heart	0.02 RPM	2.37 RPM
SRP051959_kidney	0.04 RPM	3.73 RPM
SRP051959_liver	0.04 RPM	4.07 RPM
SRP051959_lung	0.00 RPM	0.89 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.07 RPM	3.06 RPM
SRP051959_spleen	0.00 RPM	0.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_932 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_932 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_932 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011979	1 retrocopy	retro_cjac_932 ,
Homo sapiens	ENSG00000172366	1 retrocopy	retro_hsap_4901,
Gorilla gorilla	ENSGGOG00000013784	1 retrocopy	retro_ggor_43,
Nomascus leucogenys	ENSNLEG00000008117	1 retrocopy	retro_nleu_1269,
Pan troglodytes	ENSPTRG00000007548	1 retrocopy	retro_ptro_3268,
Sus scrofa	ENSSSCG00000007995	1 retrocopy	retro_sscr_433,