RetrogeneDB ID: retro_cjac_3308

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:58233389..58234191(-)
• Located in intron of: ENSCJAG00000007464

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015601
• Aliases: None
• Description: None

Sequence

>retro_cjac_3308
ATGGCAGTGAACGTATACTCAACATCAGTGACCAGCGATAATCTAAGTCGACATGACATGCTGGCCTGGATCAATGAGTC
TCTGCAGTTGAATCTGACAAAGATTGAACAGTTGTGCTCAGGGGCTGCCTATTGTCAGTTTATGGACATGCTGTTTCCTG
GCTCCATTGCCTTGAAGAAAGTGAAATTCCAAGCTAACCTAGAACACGAGTACATCTAGAACTTCAAAATACTACAAGCG
GGTTTTAAGAGGATGGGTGTTGACAAAATAATTCCTGTGGACAAATTAGTAAAAGGAAAGTTTCAGGACAATTTTGAATT
TGTTCAGTGGTTCAAGTAGTTTTTTGATGCAAACTATGATGGAAAAGACTATGACCCTGTGGCTGCCAGACAAAGTCAAG
AAACTGCAGTGGTTCCTCCCTCGTTGCTCCAGCTCTGAATAAACCAAATAAACCTCTCAGTTCTAGTAGGGCAGCTCCCC
AGAGGCCCATCTCAACACAGAGAACTGCTGCAGCTCCTAAGGCTGGCCCTGGTGTGGTGCGAAAGAACCCTGGTGTGGGC
AATGGGGAGACAAGGCAGCTGAGTTGATGCAGCAGGTCAACATATTGAAACTTACTGTTGAAGACTTGGAGAAAGAGAGG
GACTTCTACTTCGGAAAGCTACGGAACATTGAATTGATTTGCCAGGAGAATGAGGGGGAAAACGACCCTGTATTGCAGAG
GATTGTAGACATTCTGTATGCCACAGATGAAGGCTTTGTGATACCTGATGAAGGGGGCCCACAGGAGGAGCAGGAAGAGT
AT

Alignment

ORF - retro_cjac_3308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHE
          MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQA.LEHE
Retrocopy MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQANLEHE

Parental  YIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQGQETAVAP-
          YI.NFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFK.FFDANYDGKDYDPVAARQ.QETAV.P.
Retrocopy YI*NFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFK*FFDANYDGKDYDPVAARQSQETAVVP<

Parental  SLVAPALNKPKKPLSSSSAAPQRPISTQRTAAAPKAGPGVVRKNPGVGNGD-DEAAELMQQVNVLKLTVE
          SLVAPALNKP.KPLSSS.AAPQRPISTQRTAAAPKAGPGVVRKNPGVGNG..D.AAELMQQVN.LKLTVE
Retrocopy SLVAPALNKPNKPLSSSRAAPQRPISTQRTAAAPKAGPGVVRKNPGVGNGE<DKAAELMQQVNILKLTVE

Parental  DLEKERDFYFGKLRNIELICQENEGENDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY
          DLEKERDFYFGKLRNIELICQENEGENDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY
Retrocopy DLEKERDFYFGKLRNIELICQENEGENDPVLQRIVDILYATDEGFVIPDEGGPQEEQEEY

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	0.33 RPM	28.75 RPM
SRP051959_heart	0.16 RPM	18.61 RPM
SRP051959_kidney	0.20 RPM	25.65 RPM
SRP051959_liver	0.13 RPM	9.64 RPM
SRP051959_lung	0.18 RPM	25.88 RPM
SRP051959_lymph_node	0.30 RPM	28.97 RPM
SRP051959_skeletal_muscle	0.11 RPM	12.43 RPM
SRP051959_spleen	0.21 RPM	24.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3308 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3308 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013238	3 retrocopies	retro_amel_1187, retro_amel_1436, retro_amel_848,
Canis familiaris	ENSCAFG00000007306	13 retrocopies	retro_cfam_1338, retro_cfam_1554, retro_cfam_1665, retro_cfam_1804, retro_cfam_1808, retro_cfam_2084, retro_cfam_2163, retro_cfam_241, retro_cfam_547, retro_cfam_762, retro_cfam_774, retro_cfam_806, retro_cfam_913,
Choloepus hoffmanni	ENSCHOG00000006737	10 retrocopies	retro_chof_1064, retro_chof_1075, retro_chof_1113, retro_chof_1138, retro_chof_1514, retro_chof_2248, retro_chof_2557, retro_chof_2591, retro_chof_643, retro_chof_704,
Callithrix jacchus	ENSCJAG00000015601	10 retrocopies	retro_cjac_1424, retro_cjac_1647, retro_cjac_1946, retro_cjac_2077, retro_cjac_2084, retro_cjac_2366, retro_cjac_2861, retro_cjac_3259, retro_cjac_3271, retro_cjac_3308 ,
Cavia porcellus	ENSCPOG00000023542	1 retrocopy	retro_cpor_194,
Dasypus novemcinctus	ENSDNOG00000007431	2 retrocopies	retro_dnov_730, retro_dnov_822,
Erinaceus europaeus	ENSEEUG00000004499	1 retrocopy	retro_eeur_179,
Echinops telfairi	ENSETEG00000017922	4 retrocopies	retro_etel_1747, retro_etel_1778, retro_etel_2148, retro_etel_222,
Felis catus	ENSFCAG00000007783	2 retrocopies	retro_fcat_1335, retro_fcat_970,
Gorilla gorilla	ENSGGOG00000022496	1 retrocopy	retro_ggor_2765,
Loxodonta africana	ENSLAFG00000015453	1 retrocopy	retro_lafr_975,
Microcebus murinus	ENSMICG00000001965	3 retrocopies	retro_mmur_1125, retro_mmur_1179, retro_mmur_129,
Myotis lucifugus	ENSMLUG00000016403	6 retrocopies	retro_mluc_1212, retro_mluc_1811, retro_mluc_1812, retro_mluc_1883, retro_mluc_635, retro_mluc_931,
Macaca mulatta	ENSMMUG00000001816	2 retrocopies	retro_mmul_1938, retro_mmul_2374,
Monodelphis domestica	ENSMODG00000019445	3 retrocopies	retro_mdom_1213, retro_mdom_1946, retro_mdom_431,
Mustela putorius furo	ENSMPUG00000017867	3 retrocopies	retro_mputfur_1240, retro_mputfur_1304, retro_mputfur_341,
Mus musculus	ENSMUSG00000027479	2 retrocopies	retro_mmus_3160, retro_mmus_3466,
Oryctolagus cuniculus	ENSOCUG00000024265	1 retrocopy	retro_ocun_582,
Otolemur garnettii	ENSOGAG00000026557	2 retrocopies	retro_ogar_226, retro_ogar_2290,
Ochotona princeps	ENSOPRG00000006707	4 retrocopies	retro_opri_1161, retro_opri_1162, retro_opri_1212, retro_opri_807,
Pteropus vampyrus	ENSPVAG00000015887	1 retrocopy	retro_pvam_1035,
Sorex araneus	ENSSARG00000002368	1 retrocopy	retro_sara_380,
Tarsius syrichta	ENSTSYG00000000833	1 retrocopy	retro_tsyr_2018,
Tursiops truncatus	ENSTTRG00000014809	2 retrocopies	retro_ttru_1683, retro_ttru_1917,
Drosophila melanogaster	FBgn0027066	1 retrocopy	retro_dmel_83,