RetrogeneDB ID: retro_cjac_2515

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:44836655..44837203(+)
• Located in intron of: ENSCJAG00000000563

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007717
• Aliases: None
• Description: None

Sequence

>retro_cjac_2515
ATGAAGGGGTATGTGTCTAACCTAAGGGTCTGCAACCTGGTTTACAGTGGGAAGCTGGAGGAGGTGAAGGAGAGAATTCT
GGCCAATAAACCCTGGCTATGAGAACTGGCCAGGACAGCGGAAGTGCACTGCACTGGGCATGCTCAGCTGGACATATAGA
AATCGTTGAATTTTTGTTTCAACTTGGAGTGCCAGTAAAAGATAAAGACTATGCAGATTGATCTCTTCTTCAGATTGCTG
CTTCTGTGGGCCAGGATGAGACTGTAGAAGCCCTTCTGGGAAAAGGTGCTCAAGTGAATGCTGTCAATCAAAATGGCTCT
ACTCCCCTACATTCTGCAGCTTCCAAAAACAGGCATGAGATTGCTGTCATGTTACTAGAACGTGGGGCTAACCCAGATGG
TAAGGATCATTATGAGGCTACAGCAATGTACCAGGCCCCAACCAAGAGAAACTTGAAGATGATTCATATCTTTCTGTACT
ACAAAGCATCCACAAGCATCCAAGACATTGAGGGTAATACCCCTCCACACTTAGCCTATGATAAAGAG

Alignment

ORF - retro_cjac_2515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.72 %
• Parental protein coverage: 80.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGCVSNLMVCNLAYSGKLEELKESIQADK-SLATRTDQDSRTALHWACSAGHTEIVEFLLQLGVPVNDK
          M.G.VSNL.VCNL.YSGKLEE.KE.I.A.K..LA.RT.QDS..ALHWACSAGH.EIVEFL.QLGVPV.DK
Retrocopy MKGYVSNLRVCNLVYSGKLEEVKERILANK<TLAMRTGQDSGSALHWACSAGHIEIVEFLFQLGVPVKDK

Parental  DDAGWSPLHIAASAGRDEIVKALLGKGAQVNAVNQNGCTPLHYAASKNRHEIAVMLLEGGANPDAKDHYE
          D.A..S.L.IAAS.G.DE.V.ALLGKGAQVNAVNQNG.TPLH.AASKNRHEIAVMLLE.GANPD.KDHYE
Retrocopy DYAD*SLLQIAASVGQDETVEALLGKGAQVNAVNQNGSTPLHSAASKNRHEIAVMLLERGANPDGKDHYE

Parental  ATAMHRAAAKGNLKMIHILLYYKASTNIQDTEGNTPLHLACDEE
          ATAM..A..K.NLKMIHI.LYYKAST.IQD.EGNTP.HLA.D.E
Retrocopy ATAMYQAPTKRNLKMIHIFLYYKASTSIQDIEGNTPPHLAYDKE

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	2.62 RPM	10.25 RPM
SRP051959_heart	1.81 RPM	7.91 RPM
SRP051959_kidney	2.26 RPM	15.89 RPM
SRP051959_liver	1.23 RPM	7.86 RPM
SRP051959_lung	2.83 RPM	11.35 RPM
SRP051959_lymph_node	3.72 RPM	9.13 RPM
SRP051959_skeletal_muscle	1.83 RPM	4.32 RPM
SRP051959_spleen	2.86 RPM	12.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2515 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2515 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2435
Pan troglodytes	retro_ptro_1407
Gorilla gorilla	retro_ggor_1515
Pongo abelii	retro_pabe_1793

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012006	1 retrocopy	retro_acar_134,
Callithrix jacchus	ENSCJAG00000007717	1 retrocopy	retro_cjac_2515 ,
Cavia porcellus	ENSCPOG00000015068	1 retrocopy	retro_cpor_358,
Dasypus novemcinctus	ENSDNOG00000001902	5 retrocopies	retro_dnov_1194, retro_dnov_208, retro_dnov_705, retro_dnov_824, retro_dnov_835,
Homo sapiens	ENSG00000101843	3 retrocopies	retro_hsap_1214, retro_hsap_2435, retro_hsap_2737,
Gorilla gorilla	ENSGGOG00000002969	3 retrocopies	retro_ggor_1515, retro_ggor_1906, retro_ggor_945,
Microcebus murinus	ENSMICG00000002059	1 retrocopy	retro_mmur_550,
Myotis lucifugus	ENSMLUG00000014534	1 retrocopy	retro_mluc_2008,
Macaca mulatta	ENSMMUG00000016981	1 retrocopy	retro_mmul_1290,
Nomascus leucogenys	ENSNLEG00000014001	2 retrocopies	retro_nleu_243, retro_nleu_690,
Oryctolagus cuniculus	ENSOCUG00000010837	1 retrocopy	retro_ocun_793,
Otolemur garnettii	ENSOGAG00000006419	1 retrocopy	retro_ogar_213,
Procavia capensis	ENSPCAG00000005221	1 retrocopy	retro_pcap_461,
Pongo abelii	ENSPPYG00000020618	3 retrocopies	retro_pabe_1010, retro_pabe_1793, retro_pabe_2275,
Pan troglodytes	ENSPTRG00000022169	3 retrocopies	retro_ptro_1407, retro_ptro_1851, retro_ptro_831,
Ictidomys tridecemlineatus	ENSSTOG00000003783	3 retrocopies	retro_itri_1684, retro_itri_312, retro_itri_676,
Tarsius syrichta	ENSTSYG00000009920	13 retrocopies	retro_tsyr_1160, retro_tsyr_1674, retro_tsyr_1684, retro_tsyr_1741, retro_tsyr_1830, retro_tsyr_1968, retro_tsyr_1989, retro_tsyr_2010, retro_tsyr_2138, retro_tsyr_2151, retro_tsyr_2167, retro_tsyr_674, retro_tsyr_803,