RetrogeneDB ID: retro_cjac_262

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL289951.1:242687..243110(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023271
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034503
• Aliases: None
• Description: None

Sequence

>retro_cjac_262
ATGGCGGCAGCGAAGGTGAAGCAGGACATGCCCCCGGCGGGGGGCTACATCGACTACAAATGGAACTTGCTGCGTCGAGG
ACTGTCAGGCTACAGCATGCTGGCCCTGGGCATCGGGACCCTCCTCTACTGGTACTGGAAAATAATTAAGTGCAACCGCA
AACGCAGGCGCCTACAGATCAAGGACTTCAAGGCCCGCATCACGCTGATGCCACTGTTCCAGGCTGAAACGGACCGGAGG
ATCCTGCACATGCTTCGGGAGAACCTGGAAGAGGAGGCCATCATCATGAAGGACGTGACTGGCTGGAAGGTCGGGGAGTC
TGTGTTCAACCCAACTCGCTGGGTGCCCCCCTTGCTCGTGGAGTTGTACGGGCTGCGCCCCCTGGAGGAGCGTGTCTTTG
CCAACATCATGATGTACACATAG

Alignment

ORF - retro_cjac_262 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TGYSMLALGIGTLFFGYWKIIKWNRERRRLQIEDFEARIALMPLFQAETDRRILHMLRENLEEEAIIMKD
          .GYSMLALGIGTL...YWKIIK.NR.RRRLQI.DF.ARI.LMPLFQAETDRRILHMLRENLEEEAIIMKD
Retrocopy SGYSMLALGIGTLLYWYWKIIKCNRKRRRLQIKDFKARITLMPLFQAETDRRILHMLRENLEEEAIIMKD

Parental  VPGWKVGESVFNTTRWVPPLLGELYGLRPLEEAVFANHGFMMYT
          V.GWKVGESVFN.TRWVPPLL.ELYGLRPLEE.VFAN...MMYT
Retrocopy VTGWKVGESVFNPTRWVPPLLVELYGLRPLEERVFAN--IMMYT

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	13.22 RPM
SRP051959_heart	0.00 RPM	43.55 RPM
SRP051959_kidney	0.00 RPM	25.34 RPM
SRP051959_liver	0.00 RPM	25.32 RPM
SRP051959_lung	0.00 RPM	12.82 RPM
SRP051959_lymph_node	0.00 RPM	10.64 RPM
SRP051959_skeletal_muscle	0.02 RPM	47.37 RPM
SRP051959_spleen	0.00 RPM	13.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_262 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_262 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_262 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034503	1 retrocopy	retro_cjac_262 ,
Mus musculus	ENSMUSG00000036199	1 retrocopy	retro_mmus_2453,
Rattus norvegicus	ENSRNOG00000020602	2 retrocopies	retro_rnor_210, retro_rnor_629,
Sorex araneus	ENSSARG00000004735	1 retrocopy	retro_sara_693,
Sus scrofa	ENSSSCG00000013936	3 retrocopies	retro_sscr_707, retro_sscr_722, retro_sscr_739,
Tursiops truncatus	ENSTTRG00000009880	1 retrocopy	retro_ttru_1141,