RetrogeneDB ID: retro_cjac_212

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01186573.1:5311..5692(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022752
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006982
• Aliases: None
• Description: None

Sequence

>retro_cjac_212
ATGAAAGATCCAAGTCGCAGCAGTACTAGCCCAAGCATCATCAATAAAGATGTGATTATGAACGGTCATTCTCATGAAGA
TGACAATCCATTTGCAGAGTACATGTGGATGGAAAATGAAGAAGAATTCAACAGACAAATAGAAGAGGAGTTATGGGAAG
AAGAATTTATTGAACGCTGTTTCCAAGAAATGCTCGAAGAGGAAGAAGAACATGAAAGGTTTATTCCAGCTCGAGATCTC
CCACAAACTATGGACCAAATCCAAGACCAGTTTAATGACCTTGTTATCAGTGACGGCTCTTCTCTGGAAGATCTTGTGGT
CAAGAGCAATCTGAATCCAAATGCAAAGGAGTTTGTTCCTGGGGTGAAGTACTAAAATATT

Alignment

ORF - retro_cjac_212 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDPSRSSTSPSIINEDVIMNGHSHEDDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEE
          MKDPSRSSTSPSIIN.DVIMNGHSHEDDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEE
Retrocopy MKDPSRSSTSPSIINKDVIMNGHSHEDDNPFAEYMWMENEEEFNRQIEEELWEEEFIERCFQEMLEEEEE

Parental  HEWFIPARDLPQTMDQIQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY
          HE.FIPARDLPQTMDQIQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY
Retrocopy HERFIPARDLPQTMDQIQDQFNDLVISDGSSLEDLVVKSNLNPNAKEFVPGVKY

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	8.99 RPM
SRP051959_heart	0.02 RPM	18.98 RPM
SRP051959_kidney	0.07 RPM	20.15 RPM
SRP051959_liver	0.00 RPM	18.39 RPM
SRP051959_lung	0.02 RPM	19.68 RPM
SRP051959_lymph_node	0.00 RPM	17.40 RPM
SRP051959_skeletal_muscle	0.07 RPM	14.06 RPM
SRP051959_spleen	0.02 RPM	18.26 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_212 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_212 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_212 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006982	1 retrocopy	retro_cjac_212 ,
Dipodomys ordii	ENSDORG00000002264	1 retrocopy	retro_dord_676,
Microcebus murinus	ENSMICG00000012451	1 retrocopy	retro_mmur_1085,
Rattus norvegicus	ENSRNOG00000019934	1 retrocopy	retro_rnor_294,
Tupaia belangeri	ENSTBEG00000004105	1 retrocopy	retro_tbel_1370,