RetrogeneDB ID: retro_cjac_1868

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:163148160..163148854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000007730
• Aliases: None
• Description: None

Sequence

>retro_cjac_1868
ATGGTAGCGTGCAGTTACAGCTTTTCACTGACTACATTCAGCTCTCTAGTAAACTTGTCCAGATTGAATATGCTTTGTTT
CCTGTAGCTGGAGTTGCCCCATCAGTGGGAATTAAAGCTGCAAATGGTGTGGTATTAGCAAATGAGAAATAACAGAAATC
CATTCTGTATGATGAGTGAAATGTACACAAAATGGAACCAATGACCAAGCATATAGATTTGGTGTACAGTGGCATGGGCC
AAGGTTACAAAGTGCTTGTGAACAGTGCTCAAAAACTAATTCAACAATGCTATTTTGTATACCAAGAACCTATTCCCACA
GCTTATCTGGTACAGAGAGGTAGCTTCTGTGATGCAAGAATGTACTCAGGGGGTGTTTGTTCATTTGGAGTTTCTTTATT
TATTTGTGGTTGGAATGAGGGATGACCATATTTATTTCAGTCAGATCCATCTGGAGCTTACTTTGCTAGAAAGCTACAGC
AATGAGAAAGAACTATGTGGATGGAAAAACTTTCCTTGAGAAAAGATATGGTGAAGATCTGGAACTTGAAGATGGCATTC
ATACAGCCATCTTAACCCTAAAGGAAAGCTTTGAAGAGTAAATGACAGAGGATAACATAGAAGTTGGAATCTGCAATGCA
ACTGAATTTAGGAGGCTTACTCCAACTGAAGTTAAGGATTACTTGGCTGCCATA

Alignment

ORF - retro_cjac_1868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.3 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAERGYSFSLTTFSP-SGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPIT
          M....YSFSLTTFS..S.KLVQIEYAL..VAG.APSVGIKAANGVVLA.EK.QKSILYDE..VHK.EP.T
Retrocopy MVACSYSFSLTTFSS<SSKLVQIEYALFPVAGVAPSVGIKAANGVVLANEK*QKSILYDE*NVHKMEPMT

Parental  KHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICGW
          KHI.LVYSGMG..Y.VLV..A.KL.QQ.Y.VYQEPIPTA.LVQR..S.......SGGV..FGVSL.ICGW
Retrocopy KHIDLVYSGMGQGYKVLVNSAQKLIQQCYFVYQEPIPTAYLVQR-GSFCDARMYSGGVCSFGVSLFICGW

Parental  NEGRPYLFQSDPSGAYFAWK-ATAMGKNYVNGKTFLEKRYNEDLELEDAIHTAILTLKESFEGQMTEDNI
          NEG.PYLFQSDPSGAYFA.K.ATAM.KNYV.GKTFLEKRY.EDLELED.IHTAILTLKESFE..MTEDNI
Retrocopy NEG*PYLFQSDPSGAYFARK<ATAMRKNYVDGKTFLEKRYGEDLELEDGIHTAILTLKESFEE*MTEDNI

Parental  EVGICNEAGFRRLTPTEVKDYLAAI
          EVGICN...FRRLTPTEVKDYLAAI
Retrocopy EVGICNATEFRRLTPTEVKDYLAAI

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	0.13 RPM	34.66 RPM
SRP051959_heart	0.07 RPM	31.10 RPM
SRP051959_kidney	0.13 RPM	34.48 RPM
SRP051959_liver	0.69 RPM	38.90 RPM
SRP051959_lung	1.85 RPM	29.53 RPM
SRP051959_lymph_node	4.45 RPM	40.34 RPM
SRP051959_skeletal_muscle	0.04 RPM	43.92 RPM
SRP051959_spleen	1.45 RPM	41.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1868 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1868 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000990	3 retrocopies	retro_btau_296, retro_btau_384, retro_btau_889,
Choloepus hoffmanni	ENSCHOG00000000644	1 retrocopy	retro_chof_893,
Callithrix jacchus	ENSCJAG00000007730	4 retrocopies	retro_cjac_1096, retro_cjac_1868 , retro_cjac_2583, retro_cjac_852,
Cavia porcellus	ENSCPOG00000013134	1 retrocopy	retro_cpor_1512,
Dasypus novemcinctus	ENSDNOG00000011910	2 retrocopies	retro_dnov_2202, retro_dnov_724,
Echinops telfairi	ENSETEG00000015835	2 retrocopies	retro_etel_1569, retro_etel_2022,
Homo sapiens	ENSG00000106588	2 retrocopies	retro_hsap_2199, retro_hsap_908,
Gorilla gorilla	ENSGGOG00000006538	1 retrocopy	retro_ggor_735,
Myotis lucifugus	ENSMLUG00000010086	2 retrocopies	retro_mluc_1050, retro_mluc_135,
Macaca mulatta	ENSMMUG00000022451	2 retrocopies	retro_mmul_1114, retro_mmul_923,
Nomascus leucogenys	ENSNLEG00000003177	1 retrocopy	retro_nleu_329,
Oryctolagus cuniculus	ENSOCUG00000012092	1 retrocopy	retro_ocun_774,
Ochotona princeps	ENSOPRG00000011793	2 retrocopies	retro_opri_135, retro_opri_791,
Pongo abelii	ENSPPYG00000017612	2 retrocopies	retro_pabe_2076, retro_pabe_783,
Pan troglodytes	ENSPTRG00000019120	2 retrocopies	retro_ptro_1670, retro_ptro_628,
Ictidomys tridecemlineatus	ENSSTOG00000013334	1 retrocopy	retro_itri_223,
Tarsius syrichta	ENSTSYG00000014299	2 retrocopies	retro_tsyr_132, retro_tsyr_246,
Tursiops truncatus	ENSTTRG00000005649	1 retrocopy	retro_ttru_356,