RetrogeneDB ID: retro_cjac_1973

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:160391653..160392600(-)
• Located in intron of: ENSCJAG00000001269

Retrocopy information

• Ensembl ID: ENSCJAG00000034380
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012231
• Aliases: None
• Description: None

Sequence

>retro_cjac_1973
ATGGCGGGCCACCTCGTGCTCTACAACGGCGCCAAGATGCCCATCCTCGGGCTGGGCACCTGGAAGTCCCCTCCAGGCCA
AGTGACCGAGGCTGTGAAGGTGGCCATCGACGTTGGGTACCGCCACATCGACTGTGCCCATGTGTACCACAATGAGAATG
AGGTGGGGGTAACCATTCAGGAGAAGCTCAAGGAGCAGGTGGTGAAGCGTGAGGAGCTGTTCATCGTCAGCAAGCTGTGG
TGCACGTACCATGAGAAGGGCCTGGTGAAAGGAGCCTGCCTGAAGACGCTCAGCGACCTGAAGCTGGACTACCTGGACCT
CTACCTTATTCACTGGCCAACTGGCTTTAAGCCTGGGAAGGAATTTTTCCCATTGGATGAGTCAGGCAACGTGATTCCCA
GTGACACCAACATTCTGGACACGTGGGCGGCCATGGAAGAACTGGTGGATGAAGGGCTGGTGAAAGCTATTGGCATCTCC
AACTTCAACCATCTCCAGGTGGAGAGGATCTTAAACAAACTGGCTTAAAGTATAAGCCTGCAGTTAACCAGATTGAGTGC
CACCCATACCTCACTCAGGAGAAGTTAATCCAGTACTGCCAGTCCAAAGGCATCGTGGTGACCGCCTACAGCCCCCTAGG
CTCTCCCGACAGGCCCTGGGCCAAGCCCGAGGACCCTTCCCTCCTGGAGGATCCCAGGATCAAGGCGATCGCAGACAAGC
ACAATAAAACCACAGCTCAGGTGCTGATCCGGTTCCCCATGCAGAGGAACTTGGTGGTGATCCCCAAGTCTGTGACACCA
GAACGCATTGCTGAGAACTTTAAGGTCTTTGACTTTGAACTGAGCAGCGAGGATATGACCACCTTACTCGGCTACAACAG
GAACTGGAGGGTCTGTGCCTTGGTGAGCGCTGTCTCCCACAAGGATTACCCCTTCCATGAAGAGTTT

Alignment

ORF - retro_cjac_1973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGHLVLYNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYHNENEVGVAIQEKLKEQVVKR
          MAGHLVLYNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYHNENEVGV.IQEKLKEQVVKR
Retrocopy MAGHLVLYNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYHNENEVGVTIQEKLKEQVVKR

Parental  EELFIVSKLWCTYHEKGLVKGACLKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVIPSDTNILD
          EELFIVSKLWCTYHEKGLVKGACLKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVIPSDTNILD
Retrocopy EELFIVSKLWCTYHEKGLVKGACLKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVIPSDTNILD

Parental  TWAAMEELVDEGLVKAIGISNFNHLQVERILNK-PGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTA
          TWAAMEELVDEGLVKAIGISNFNHLQVERILNK..GLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTA
Retrocopy TWAAMEELVDEGLVKAIGISNFNHLQVERILNK<TGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTA

Parental  YSPLGSPDRPWAKPEDPSLLEDPRIKAIADKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDF
          YSPLGSPDRPWAKPEDPSLLEDPRIKAIADKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDF
Retrocopy YSPLGSPDRPWAKPEDPSLLEDPRIKAIADKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDF

Parental  ELSSEDMTTLLGYNRNWRVCALMSAVSHKDYPFHEEF
          ELSSEDMTTLLGYNRNWRVCAL.SAVSHKDYPFHEEF
Retrocopy ELSSEDMTTLLGYNRNWRVCALVSAVSHKDYPFHEEF

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	0.24 RPM	8.36 RPM
SRP051959_heart	0.16 RPM	19.91 RPM
SRP051959_kidney	0.11 RPM	20.59 RPM
SRP051959_liver	0.00 RPM	9.40 RPM
SRP051959_lung	0.28 RPM	16.95 RPM
SRP051959_lymph_node	0.23 RPM	16.94 RPM
SRP051959_skeletal_muscle	0.11 RPM	24.87 RPM
SRP051959_spleen	0.44 RPM	55.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1973 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1973 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009902	3 retrocopies	retro_btau_1092, retro_btau_1642, retro_btau_821,
Canis familiaris	ENSCAFG00000001290	1 retrocopy	retro_cfam_63,
Callithrix jacchus	ENSCJAG00000012231	14 retrocopies	retro_cjac_1140, retro_cjac_1167, retro_cjac_1718, retro_cjac_1973 , retro_cjac_2550, retro_cjac_3102, retro_cjac_3143, retro_cjac_3297, retro_cjac_3692, retro_cjac_3840, retro_cjac_3872, retro_cjac_3910, retro_cjac_476, retro_cjac_621,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Callithrix jacchus	ENSCJAG00000012872	1 retrocopy	retro_cjac_1688,
Callithrix jacchus	ENSCJAG00000013633	2 retrocopies	retro_cjac_3093, retro_cjac_3334,
Dasypus novemcinctus	ENSDNOG00000011358	2 retrocopies	retro_dnov_2214, retro_dnov_721,
Homo sapiens	ENSG00000085662	7 retrocopies	retro_hsap_1261, retro_hsap_1422, retro_hsap_2049, retro_hsap_2663, retro_hsap_312, retro_hsap_4745, retro_hsap_851,
Gorilla gorilla	ENSGGOG00000011731	6 retrocopies	retro_ggor_1477, retro_ggor_1859, retro_ggor_2948, retro_ggor_343, retro_ggor_695, retro_ggor_991,
Macropus eugenii	ENSMEUG00000003434	6 retrocopies	retro_meug_1455, retro_meug_1505, retro_meug_1811, retro_meug_1980, retro_meug_486, retro_meug_504,
Microcebus murinus	ENSMICG00000001921	2 retrocopies	retro_mmur_1087, retro_mmur_66,
Mus musculus	ENSMUSG00000001642	10 retrocopies	retro_mmus_1252, retro_mmus_2082, retro_mmus_2678, retro_mmus_3242, retro_mmus_3488, retro_mmus_444, retro_mmus_534, retro_mmus_764, retro_mmus_784, retro_mmus_920,
Nomascus leucogenys	ENSNLEG00000013037	7 retrocopies	retro_nleu_1246, retro_nleu_1533, retro_nleu_2099, retro_nleu_2569, retro_nleu_2570, retro_nleu_418, retro_nleu_419,
Otolemur garnettii	ENSOGAG00000016156	2 retrocopies	retro_ogar_1282, retro_ogar_808,
Procavia capensis	ENSPCAG00000016195	1 retrocopy	retro_pcap_428,
Pongo abelii	ENSPPYG00000018017	8 retrocopies	retro_pabe_1050, retro_pabe_1089, retro_pabe_1176, retro_pabe_1672, retro_pabe_2411, retro_pabe_3691, retro_pabe_370, retro_pabe_694,
Pan troglodytes	ENSPTRG00000019716	6 retrocopies	retro_ptro_1365, retro_ptro_1794, retro_ptro_254, retro_ptro_3040, retro_ptro_3160, retro_ptro_972,
Rattus norvegicus	ENSRNOG00000009513	1 retrocopy	retro_rnor_1438,
Tupaia belangeri	ENSTBEG00000013327	1 retrocopy	retro_tbel_3093,