RetrogeneDB ID: retro_cjac_192

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:60571876..60572410(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023045
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000004753
• Aliases: None
• Description: None

Sequence

>retro_cjac_192
ATGGCCACTAACTACAGTGCCAACCAGTATGAAAAGGCTTTCTCATCCAAGTATCTGCAGAACTGGTCTCCCACTAAGCC
AACAAAAGAGTATATCTCTTCCCATGAAGGCTACACTCAAATTATTGCCAATGATCGTGGTCATCTACTGCCTTCTGTGC
CCCGTTCCAAGGCAAATCCTTGGGGTTCCTTCATGGGCACCTGGCAAATGCCTCTGAAGATACCCCCTGCTCGGGTGACA
CTGACTTCCCGTACAACTGCTGGTGCTGCCTCCCTTACCAAATGGATACAGAAAAATCCTGATTTACTCAAGGCCTCCAA
TGGGCTGCGTCCTGAAATCTTAGGCAAGTCCCATGATCCAGACAGTCAGAAGACATTCAGGAAGAAGTCTATCACAAAGA
CTGTACAACAAGCACCAAGTCCAACCGTAATTCCACGCTCCCCAGCTGCCAACCTCAATTCCCCAGATGAACTCCAAAGC
TCACACCCCTCTGCAGGTCATACTCCAGGTCCCCAAAGCCCAGCAAAATCCTAA

Alignment

ORF - retro_cjac_192 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATNYSANQYEKAFSSKYLQNWSPAKPTKESISSHEGYTQIIANDRGHLLPSVPRSKANPWGSFMGTWQM
          MATNYSANQYEKAFSSKYLQNWSP.KPTKE.ISSHEGYTQIIANDRGHLLPSVPRSKANPWGSFMGTWQM
Retrocopy MATNYSANQYEKAFSSKYLQNWSPTKPTKEYISSHEGYTQIIANDRGHLLPSVPRSKANPWGSFMGTWQM

Parental  PLKIPPARVTLTSRTTAGAASLTKWIQKNPDLLKASNGLRPEILGKSHDPDSQKTFRKKSITKTVQQAPS
          PLKIPPARVTLTSRTTAGAASLTKWIQKNPDLLKASNGLRPEILGKSHDPDSQKTFRKKSITKTVQQAPS
Retrocopy PLKIPPARVTLTSRTTAGAASLTKWIQKNPDLLKASNGLRPEILGKSHDPDSQKTFRKKSITKTVQQAPS

Parental  PTVIPRSPAANLNSPDELQSSHPSAGHTPGPQSPAKS
          PTVIPRSPAANLNSPDELQSSHPSAGHTPGPQSPAKS
Retrocopy PTVIPRSPAANLNSPDELQSSHPSAGHTPGPQSPAKS

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	1.97 RPM
SRP051959_heart	0.00 RPM	2.56 RPM
SRP051959_kidney	0.00 RPM	1.80 RPM
SRP051959_liver	0.00 RPM	1.34 RPM
SRP051959_lung	0.05 RPM	1.97 RPM
SRP051959_lymph_node	0.00 RPM	1.35 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.40 RPM
SRP051959_spleen	0.00 RPM	1.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_192 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_192 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004753	1 retrocopy	retro_cjac_192 ,
Echinops telfairi	ENSETEG00000011522	1 retrocopy	retro_etel_834,
Tupaia belangeri	ENSTBEG00000015510	1 retrocopy	retro_tbel_1205,