RetrogeneDB ID: retro_cjac_2208

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:6515735..6516269(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012315
• Aliases: None
• Description: None

Sequence

>retro_cjac_2208
ATGCCCAAGGCCAAGGGCAAGACCCGGAGGCAGAAGTTTGGTTACAATGTCAACCGAAAGCGTCTGAAGCGGAATGCTCG
ACGGAAGGCAGCGCCGCGGATCGGGTGCTCACATATGTGACATGCCTGGGACCACGCCAAATCCATGCGGCTGAACCTGG
CCGAGATGGGGTTGGCTGTGGACCCCAACGAGACGGTGCCCCTCCGTAAGAGAAAGGTGAAGGTCATGGAGGTGGACATA
GCGGCGAGCCCTAAGGAGCTTGTGCAGAAGCCCTATGTGCTGAATGACATGGAGGCAGAAGCCAGCCTCCCAGAAAAGAA
AGGAAATACTCCGTCTCGGGACCACATCGACTACATACACTACATGGTGGAGAACCACGGGGAGGACTATAAGGCCATGG
CCCACGATGAGAAGAATTGCTATCAAGATACCCCAAAACAGATTCGGAATAAGCTCCATGTCTACGAACGCGTTTACCCA
GTAGAGTGGCAAGACTGCCTCGATTCTTTGCAGAAGAATAAGATGGAGCTTGAG

Alignment

ORF - retro_cjac_2208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKAKGKTRRQKFGYNVNRKRLNRNARRKAAPRIECSHIRHAWDHAKSVRQNLAEMGLAVDPNKAVPLRK
          MPKAKGKTRRQKFGYNVNRKRL.RNARRKAAPRI.CSH..HAWDHAKS.R.NLAEMGLAVDPN..VPLRK
Retrocopy MPKAKGKTRRQKFGYNVNRKRLKRNARRKAAPRIGCSHM*HAWDHAKSMRLNLAEMGLAVDPNETVPLRK

Parental  RKVKVMEVDIEERPKELVRKPYVLNDLEAEASLPEKKGNTLSRDLIDYVRYMVENHGEDYKAMARDEKNY
          RKVKVMEVDI...PKELV.KPYVLND.EAEASLPEKKGNT.SRD.IDY..YMVENHGEDYKAMA.DEKN.
Retrocopy RKVKVMEVDIAASPKELVQKPYVLNDMEAEASLPEKKGNTPSRDHIDYIHYMVENHGEDYKAMAHDEKNC

Parental  YQDTPKQIRNKINVYKRFYPAEWQDFLDSLQKNKMEVE
          YQDTPKQIRNK..VY.R.YP.EWQD.LDSLQKNKME.E
Retrocopy YQDTPKQIRNKLHVYERVYPVEWQDCLDSLQKNKMELE

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	2.86 RPM
SRP051959_heart	0.00 RPM	4.35 RPM
SRP051959_kidney	0.00 RPM	6.26 RPM
SRP051959_liver	0.02 RPM	7.67 RPM
SRP051959_lung	0.03 RPM	3.81 RPM
SRP051959_lymph_node	0.00 RPM	4.04 RPM
SRP051959_skeletal_muscle	0.04 RPM	6.38 RPM
SRP051959_spleen	0.00 RPM	3.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2208 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2208 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016694	2 retrocopies	retro_cfam_1790, retro_cfam_1793,
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208 ,
Cavia porcellus	ENSCPOG00000026072	1 retrocopy	retro_cpor_129,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Myotis lucifugus	ENSMLUG00000003504	1 retrocopy	retro_mluc_2425,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Mus musculus	ENSMUSG00000025869	2 retrocopies	retro_mmus_3033, retro_mmus_3258,
Otolemur garnettii	ENSOGAG00000000824	2 retrocopies	retro_ogar_1323, retro_ogar_2299,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,
Ictidomys tridecemlineatus	ENSSTOG00000004869	1 retrocopy	retro_itri_1124,