RetrogeneDB ID: retro_cjac_1800

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:61931990..61932600(+)
• Located in intron of: ENSCJAG00000007009

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003670
• Aliases: None
• Description: None

Sequence

>retro_cjac_1800
AGAGACAAGGTGGTGCTGGAAATGGGCTCAGGCACAGGCATCTTCTGCATGTTCGCCACCAAGGTTGGGGCCTGGAAGGT
CATCGGGATTGAGTGGTCCAGAATCTCTGATTATGCGGTGAATATTGTCAAAGCCAACAAGTTAGACCACATGGTGACCA
TCATCAAAGGGAAGCTGGAGGAAGTAGAGCTCCGGGTGGAAAAGGTGGACATCATTATCAGCGAGCGGATGGGCTACTGC
CTCTTATACGAGTCCATGTTCTACGCCCAGGACAAGTGGCTGGTGCCTGATATTCTCATCTTCCCAGACCAGGCCACACT
GTAATGTGATGGCCATCGAGGACTGGCAGTACAAAGACTACAAGATCCACTGGTGGGAAAACGTGTATGGCTTCGACATG
TCTTGCATCTAAGATGTGGCCATCAAGGAGCCCCTAGTGGACGTGGTGGATCCCAAACAGCTGGTCATCAATACTTGCCT
CATAAAGGAGGGGGACATCAACACCATCAAGGAGAAAGACCTGACCTTCACCTCCCTATTCTGCCTACAAGTGAAGCAGA
ATGACTATGTGCATGCCCTGGTGGTCTACTTTGAGTTCAGTGCCACAAGA

Alignment

ORF - retro_cjac_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 58.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDKVVLDVGSGTGILCMFAAKAGARKVIGIECSSISDYAVKIVKANKLDHVVTIIKGKVEEVELPVEKVD
          .DKVVL..GSGTGI.CMFA.K.GA.KVIGIE.S.ISDYAV.IVKANKLDH.VTIIKGK.EEVEL.VEKVD
Retrocopy RDKVVLEMGSGTGIFCMFATKVGAWKVIGIEWSRISDYAVNIVKANKLDHMVTIIKGKLEEVELRVEKVD

Parental  IIISEWMGYCLFYESMLNTVLYARDKWLAPDGLIFPDRATL-YVTAIEDRQYKDYKIHWWENVYGFDMSC
          IIISE.MGYCL.YESM.....YA.DKWL.PD.LIFPD.ATL..V.AIED.QYKDYKIHWWENVYGFDMSC
Retrocopy IIISERMGYCLLYESMF----YAQDKWLVPDILIFPDQATL>NVMAIEDWQYKDYKIHWWENVYGFDMSC

Parental  IKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYTVKVEDLTFTSPFCLQVKRNDYVHALVAYFNIEFTR
          I.DVAIKEPLVDVVDPKQLV.N.CLIKE.DI.T.K..DLTFTS.FCLQVK.NDYVHALV.YF....TR
Retrocopy I*DVAIKEPLVDVVDPKQLVINTCLIKEGDINTIKEKDLTFTSLFCLQVKQNDYVHALVVYFEFSATR

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	0.67 RPM	11.91 RPM
SRP051959_heart	0.54 RPM	18.26 RPM
SRP051959_kidney	0.84 RPM	12.80 RPM
SRP051959_liver	0.41 RPM	7.69 RPM
SRP051959_lung	1.04 RPM	11.83 RPM
SRP051959_lymph_node	1.60 RPM	14.59 RPM
SRP051959_skeletal_muscle	0.55 RPM	20.09 RPM
SRP051959_spleen	0.82 RPM	11.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1800 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1800 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3406
Pan troglodytes	retro_ptro_2313
Gorilla gorilla	retro_ggor_2305
Pongo abelii	retro_pabe_2804
Macaca mulatta	retro_mmul_2121

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800 , retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077, retro_rnor_2668,