RetrogeneDB ID: retro_cjac_2989

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:74206665..74207241(-)
• Located in intron of: ENSCJAG00000002566

Retrocopy information

• Ensembl ID: ENSCJAG00000002618
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000013012
• Aliases: None
• Description: None

Sequence

>retro_cjac_2989
ATGCAGGCTGTAAGAAACGCAGGGTCGTGTCTCCTGTGGACTTGGCCCCCAGACAACTGGGGTCATGGTCAGGACGCCGG
CCCGGATCATCCACACAGGCGCCCGGCAGCTGCAAGACACTGCGGTCAAGCAGGAAGTTGAAGAGAAGACGGCAGCTCCC
AGACACACCAGCTTCAGCATTTACCCTCCTATTCCAGGAGAGGAGAGCTCTCTGAAGTGGGCAGGAAAGAAGTTTGAGGA
GATCCCAATCACACACATTAAAGCATCCTACAACAACACACAGATCCAGGTAGTCTCTGCCAGTAACCAGCCCCTTGGCC
ATGCTTCCTGTGGCACAGAGGGATTTTGGAATGCCAGGAAGGGCACAAGCATCACAGCACAGACAGCAGGCATAGCCGCA
GCGGCGAAAGCTATCCAAAAGGGTGTGACCCACATCCGAGTTGTGGTGAAAGGCCTGGGGCCAGGACGCTTGTCTGCCAT
CAGTGGACTGACCATGGGGGCCTGGAAGTGATCTTAATCACAGACAACACCCCCATCCCGCACAACGGCTGCTGTCCCAG
GAAGGCTCAGAGGCTG

Alignment

ORF - retro_cjac_2989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQAVRNAGSWLLRSWPP-TSGRVVARTAARTIHTGARQLQDAAAKQEVEEKSAAPRHTSFSIYPPIPGEE
          MQAVRNAGS.LL..WPP.T.G.V..RT.AR.IHTGARQLQD.A.KQEVEEK.AAPRHTSFSIYPPIPGEE
Retrocopy MQAVRNAGSCLLWTWPP>TTG-VMVRTPARIIHTGARQLQDTAVKQEVEEKTAAPRHTSFSIYPPIPGEE

Parental  SSLRWAGKKFEEIPIAHIKASYNNTQIQVLSASNQPLAHASCGTEGFRNARKGTGIAAQTAGIAAAAKAI
          SSL.WAGKKFEEIPI.HIKASYNNTQIQV.SASNQPL.HASCGTEGF.NARKGT.I.AQTAGIAAAAKAI
Retrocopy SSLKWAGKKFEEIPITHIKASYNNTQIQVVSASNQPLGHASCGTEGFWNARKGTSITAQTAGIAAAAKAI

Parental  QKGVTHIRVVVKGLGPGRLSAINGLTM-GGLEVISITDNTPIPHNGCRPRKARRL
          QKGVTHIRVVVKGLGPGRLSAI.GLTM.GGLEVI.ITDNTPIPHNGC.PRKA.RL
Retrocopy QKGVTHIRVVVKGLGPGRLSAISGLTM<GGLEVILITDNTPIPHNGCCPRKAQRL

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	0.04 RPM	4.24 RPM
SRP051959_heart	0.02 RPM	5.79 RPM
SRP051959_kidney	0.02 RPM	5.99 RPM
SRP051959_liver	0.02 RPM	5.07 RPM
SRP051959_lung	0.08 RPM	4.08 RPM
SRP051959_lymph_node	0.05 RPM	4.93 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.57 RPM
SRP051959_spleen	0.06 RPM	5.15 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2989 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2989 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2989 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601, retro_cjac_2989 ,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808, retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419,