RetrogeneDB ID: retro_cjac_165

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:170098179..170098548(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022891
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000014890
• Aliases: None
• Description: None

Sequence

>retro_cjac_165
ATGACTTCCCCTGAAATTGCTTCCTTATCATGGGGGCAAATGAAAGTACAAGGCTCTAATACAACCTATAAGGACTGCAA
AGTATGGCCAGGGGGTAGTCGGACTTGGGATTGGAGAGAAACAGGAACTGAGCATTCTCCTGGAGTGCAGCCTGCAGATG
TGAAGGAAGTTGTTGAGAAAGGTATACAGACTCTTGTGATTGGCCGAGGGATGAGTGAGGCCTTGAAGTTTCCTTCATCA
ACTGTGGAGTACCTCAAGAAACATGGCATTGATGTGCAGGTCCTCCAGACAGAGCAGGCAGTGAAGGAGTATAATGCCTT
GGTTGCCCAAGGGGTCAGGGTGGGAGGTGTCTTCCATTCCACCTGCTGA

Alignment

ORF - retro_cjac_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTSPEIASLSWGQMKVQGSNTTYKDCKVWPGGSRTWDWRETGTEHSPGVQPADVKEVVEKGIQTLVIGRG
          MTSPEIASLSWGQMKVQGSNTTYKDCKVWPGGSRTWDWRETGTEHSPGVQPADVKEVVEKGIQTLVIGRG
Retrocopy MTSPEIASLSWGQMKVQGSNTTYKDCKVWPGGSRTWDWRETGTEHSPGVQPADVKEVVEKGIQTLVIGRG

Parental  MSEALKVPSSTVEYLKKHGIDVRVLQTEQAVKEYNALVAQGVRVGGVFHSTC
          MSEALK.PSSTVEYLKKHGIDV.VLQTEQAVKEYNALVAQGVRVGGVFHSTC
Retrocopy MSEALKFPSSTVEYLKKHGIDVQVLQTEQAVKEYNALVAQGVRVGGVFHSTC

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	2.11 RPM
SRP051959_heart	0.00 RPM	8.33 RPM
SRP051959_kidney	0.13 RPM	13.42 RPM
SRP051959_liver	0.06 RPM	16.59 RPM
SRP051959_lung	0.00 RPM	4.52 RPM
SRP051959_lymph_node	0.00 RPM	2.26 RPM
SRP051959_skeletal_muscle	0.07 RPM	7.88 RPM
SRP051959_spleen	0.02 RPM	4.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_165 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_165 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002128	1 retrocopy	retro_amel_1604,
Callithrix jacchus	ENSCJAG00000014890	1 retrocopy	retro_cjac_165 ,
Echinops telfairi	ENSETEG00000006423	1 retrocopy	retro_etel_187,
Felis catus	ENSFCAG00000007450	1 retrocopy	retro_fcat_8,
Loxodonta africana	ENSLAFG00000000518	1 retrocopy	retro_lafr_784,
Microcebus murinus	ENSMICG00000000300	2 retrocopies	retro_mmur_157, retro_mmur_424,
Mustela putorius furo	ENSMPUG00000015932	1 retrocopy	retro_mputfur_1468,
Rattus norvegicus	ENSRNOG00000012584	1 retrocopy	retro_rnor_2097,
Tarsius syrichta	ENSTSYG00000002262	1 retrocopy	retro_tsyr_1886,
Tursiops truncatus	ENSTTRG00000007111	1 retrocopy	retro_ttru_406,