RetrogeneDB ID: retro_cjac_2548

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:102584995..102585371(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012116
• Aliases: None
• Description: None

Sequence

>retro_cjac_2548
GAAGAGAGCTTTACTCTGTCCTTCTCAGCCTCTGATGCAGAAATTGACACGATGGTTGCATAATTAGAGGACATTATCAT
GGATGACAAGTTCCATTTATTACAGAGAAACTTCATAGAAAAGTACTACCTGGAGTTTTGAAAATACAGAAGCGAATAAA
CTCACCTACATGCCTAGTTTTAATAAGTATATTTTTTTGGAGAGAAAATATGATGAAGAATAGCAGAAGATTCCTGGATT
CAACACTGCAGTTTTCACAACTACATTACAGCATCATAAAGGTGAAGTGGCTGGTAACATATTCGACATGCTGCCCACCT
TTACTGATGTTTTAGCTTTTACAGAAATGCTTTTGGACTACAGAGCAGAAAAGGAA

Alignment

ORF - retro_cjac_2548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EESFALSFSSASDAEFDAVVGYLEDIIMDDKFQLLQRNFMDKYYLEF-EDTEENKLTYTPIFNEYISLVE
          EESF.LSFS.ASDAE.D..V..LEDIIMDDKF.LLQRNF..KYYLEF.E.TE.NKLTY.P.FN.YI.L..
Retrocopy EESFTLSFS-ASDAEIDTMVA*LEDIIMDDKFHLLQRNFIEKYYLEF>ENTEANKLTYMPSFNKYIFLER

Parental  KYVEEQLLERIPGFNMAAFTVTLQHHRDEVAGDIFDMLLTFTDFLAFKEMFLDYRAEKE
          KY.EE.....IPGFN.A.FT.TLQHH..EVAG.IFDML.TFTD.LAF.EM.LDYRAEKE
Retrocopy KYDEE*--QKIPGFNTAVFTTTLQHHKGEVAGNIFDMLPTFTDVLAFTEMLLDYRAEKE

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	0.00 RPM	5.59 RPM
SRP051959_heart	0.00 RPM	8.37 RPM
SRP051959_kidney	0.00 RPM	8.39 RPM
SRP051959_liver	0.00 RPM	1.86 RPM
SRP051959_lung	0.00 RPM	11.22 RPM
SRP051959_lymph_node	0.00 RPM	6.89 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.45 RPM
SRP051959_spleen	0.00 RPM	5.86 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2548 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2548 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 31 parental genes, and 133 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004844	1 retrocopy	retro_btau_362,
Canis familiaris	ENSCAFG00000008785	3 retrocopies	retro_cfam_1026, retro_cfam_1235, retro_cfam_1357,
Choloepus hoffmanni	ENSCHOG00000009016	16 retrocopies	retro_chof_1180, retro_chof_1220, retro_chof_1287, retro_chof_1526, retro_chof_1655, retro_chof_1677, retro_chof_1858, retro_chof_1904, retro_chof_2024, retro_chof_2189, retro_chof_2247, retro_chof_2646, retro_chof_2658, retro_chof_408, retro_chof_500, retro_chof_977,
Callithrix jacchus	ENSCJAG00000012116	9 retrocopies	retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548 , retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625, retro_cjac_689,
Cavia porcellus	ENSCPOG00000011406	5 retrocopies	retro_cpor_1501, retro_cpor_203, retro_cpor_249, retro_cpor_299, retro_cpor_571,
Dipodomys ordii	ENSDORG00000016342	2 retrocopies	retro_dord_227, retro_dord_579,
Equus caballus	ENSECAG00000016621	3 retrocopies	retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus	ENSFCAG00000002937	3 retrocopies	retro_fcat_400, retro_fcat_69, retro_fcat_974,
Homo sapiens	ENSG00000102931	7 retrocopies	retro_hsap_1189, retro_hsap_1846, retro_hsap_3237, retro_hsap_3263, retro_hsap_3270, retro_hsap_4293, retro_hsap_999,
Gorilla gorilla	ENSGGOG00000005471	5 retrocopies	retro_ggor_2159, retro_ggor_2202, retro_ggor_2222, retro_ggor_2868, retro_ggor_927,
Loxodonta africana	ENSLAFG00000008633	3 retrocopies	retro_lafr_103, retro_lafr_228, retro_lafr_418,
Microcebus murinus	ENSMICG00000012467	6 retrocopies	retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Myotis lucifugus	ENSMLUG00000012680	3 retrocopies	retro_mluc_1338, retro_mluc_1843, retro_mluc_746,
Macaca mulatta	ENSMMUG00000020352	7 retrocopies	retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica	ENSMODG00000013511	1 retrocopy	retro_mdom_1182,
Mustela putorius furo	ENSMPUG00000004306	2 retrocopies	retro_mputfur_1046, retro_mputfur_1369,
Nomascus leucogenys	ENSNLEG00000002803	7 retrocopies	retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Oryctolagus cuniculus	ENSOCUG00000000582	1 retrocopy	retro_ocun_431,
Otolemur garnettii	ENSOGAG00000014535	9 retrocopies	retro_ogar_1448, retro_ogar_1476, retro_ogar_1657, retro_ogar_1658, retro_ogar_1919, retro_ogar_2427, retro_ogar_2475, retro_ogar_3184, retro_ogar_3352,
Ochotona princeps	ENSOPRG00000006931	2 retrocopies	retro_opri_675, retro_opri_98,
Procavia capensis	ENSPCAG00000005664