RetrogeneDB ID: retro_cjac_117

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:121009102..121010044(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022413
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RRAGB
• Ensembl ID: ENSCJAG00000007317
• Aliases: None
• Description: None

Sequence

>retro_cjac_117
ATGCCAAATACAGCCATGAAGAAAAAGGTGCTACTGATGGGGAAGAGCGGGTCGGGGAAGACCAGCATGAGGTCGATTAT
CTTCGCCAATTATATTGCTCGCGACACCCGGCGCCTGGGGGCCACCATTGACGTGGAGCACTCCCACGTCCGATTCCTGG
GGAACCTGGTGCTGAACCTGTGGGACTGTGGCGGTCAGGACACCTTCATGGAAAATTACTTCACCAGCCAGCGAGACAAC
ATCTTCCGTAACGTAGAGGTTTTGATTTACGTGTTTGACGTGGAGAGCCGTGAACTGGAGAAGGATATGCATTATTACCA
GTCATGTCTGGAGGCCATCCTCCAGAACTCTCCTGACGCCAAAATCTTCTGCCTGGTGCACAAAATGGATCTGGTTCAGG
AGGATCAGCGCGACCTGATTTTTAAAGAGCGAGAGGAAGACCTGAGGCGTCTGTCTCGCCCGCTGGAGTGTGCTTGTTTT
CGAACGTCCATCTGGGATGAGACGCTCTACAAAGCCTGGTCCAGCATCGTCTACCAGCTGATTCCCAACGTTCAGCAGCT
GGAGATGAACCTCAGGAATTTTGCCCAAATCATCGAGGCCGATGAAGTTCTGCTGTTCGAAAGAGCTACGTTCTTGGTTA
TTTCCCACTACCAGTGCAAAGAGCAGCGCGACGTCCACCGGTTTGAGAAGATCAGCAACATCATCAAGCAGTTCAAGCTG
AGCTGCAGTAAATTGGCCGCTTCCTTTCAGAGCATGGAAGTTAGGAATTCCAACTTCGCGGCTTTCATCGACATCTTCAC
CTCAAACACGTACGTGATGGTGGTCATGTCAGATCCGTCGATCCCTTCTGCGGCCACCCTGATCAACATTCGCAATGCCA
GGAAACACTTTGAGAAGCTGGAGAGAGTGGATGGCCCCAAGCACAGTCTCCTCATGCGTTGA

Alignment

ORF - retro_cjac_117 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.76 %
• Parental protein coverage: 90.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPNAAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
          .PN.AMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM
Retrocopy MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDTFM

Parental  ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
          ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI
Retrocopy ENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDAKIFCLVHKMDLVQEDQRDLI

Parental  FKEREEDLRRLSRPLECSCFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAEIIEADEVLLFERAT
          FKEREEDLRRLSRPLEC.CFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFA.IIEADEVLLFERAT
Retrocopy FKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQLIPNVQQLEMNLRNFAQIIEADEVLLFERAT

Parental  FLVISHYQCKEQRDAHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
          FLVISHYQCKEQRD.HRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS
Retrocopy FLVISHYQCKEQRDVHRFEKISNIIKQFKLSCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPS

Parental  IPSAATLINIRNARKHFEKLERVDGPKQCLLMR
          IPSAATLINIRNARKHFEKLERVDGPK..LLMR
Retrocopy IPSAATLINIRNARKHFEKLERVDGPKHSLLMR

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	0.87 RPM	2.66 RPM
SRP051959_heart	1.84 RPM	6.21 RPM
SRP051959_kidney	1.24 RPM	7.28 RPM
SRP051959_liver	1.13 RPM	3.90 RPM
SRP051959_lung	1.22 RPM	5.95 RPM
SRP051959_lymph_node	0.96 RPM	5.16 RPM
SRP051959_skeletal_muscle	1.16 RPM	6.73 RPM
SRP051959_spleen	1.32 RPM	6.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_117 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_117 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_117 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4
Pan troglodytes	retro_ptro_48
Pongo abelii	retro_pabe_191
Macaca mulatta	retro_mmul_249
Mus musculus	retro_mmus_159
Sus scrofa	retro_sscr_15
Canis familiaris	retro_cfam_421
Equus caballus	retro_ecab_608

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012920	1 retrocopy	retro_amel_1842,
Canis familiaris	ENSCAFG00000016503	1 retrocopy	retro_cfam_421,
Callithrix jacchus	ENSCJAG00000007317	1 retrocopy	retro_cjac_117 ,
Cavia porcellus	ENSCPOG00000011266	1 retrocopy	retro_cpor_86,
Equus caballus	ENSECAG00000006020	1 retrocopy	retro_ecab_608,
Felis catus	ENSFCAG00000013932	1 retrocopy	retro_fcat_21,
Homo sapiens	ENSG00000083750	1 retrocopy	retro_hsap_4,
Gorilla gorilla	ENSGGOG00000011501	1 retrocopy	retro_ggor_65,
Loxodonta africana	ENSLAFG00000016144	1 retrocopy	retro_lafr_102,
Myotis lucifugus	ENSMLUG00000015720	1 retrocopy	retro_mluc_40,
Macaca mulatta	ENSMMUG00000017635	1 retrocopy	retro_mmul_249,
Mustela putorius furo	ENSMPUG00000003730	1 retrocopy	retro_mputfur_87,
Mus musculus	ENSMUSG00000041658	1 retrocopy	retro_mmus_159,
Nomascus leucogenys	ENSNLEG00000016350	1 retrocopy	retro_nleu_13,
Oryctolagus cuniculus	ENSOCUG00000008666	1 retrocopy	retro_ocun_166,
Otolemur garnettii	ENSOGAG00000000345	1 retrocopy	retro_ogar_675,
Procavia capensis	ENSPCAG00000003417	1 retrocopy	retro_pcap_6,
Pongo abelii	ENSPPYG00000020398	1 retrocopy	retro_pabe_191,
Pan troglodytes	ENSPTRG00000021955	1 retrocopy	retro_ptro_48,
Rattus norvegicus	ENSRNOG00000003160	1 retrocopy	retro_rnor_2,
Sus scrofa	ENSSSCG00000029800	1 retrocopy	retro_sscr_15,