RetrogeneDB ID: retro_cjac_1104

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:60615945..60616662(+)
• Located in intron of: ENSCJAG00000020550

Retrocopy information

• Ensembl ID: ENSCJAG00000020549
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DRG1
• Ensembl ID: ENSCJAG00000011009
• Aliases: None
• Description: None

Sequence

>retro_cjac_1104
ATGAGCAGCACCTTGGCTAAGATCATGGAGATAGAAGCTGAGATGGCTCGGACTCAAAAGAACAAAGCCACAGCATACCA
CCTAGAGCTGCTTAAGGGTGGTCTTGCTGAGCTTCGTCAAGAACTCATTACTCCAAAGGGTGGTGGTGGTGGAAGTCCAG
GAGAAGGTTTTGATGTGGCCAAGACAGGTGATGCGCGAATTGGATTTGTTGGTTTTCCATCTGCGGGGAAGTCAACACTG
CTTAGTAACCTGGCAGGGGTGTATTCTGAGGTAGCAGCCTATGAATTCGCTACTCTGACCACCATGCCTGGTGTCATCAG
ATACAAAGGTGCCAAGATCCAGCTCCTGGATCTCCCAGGTATCATCGAAGGTGCCAAGGATGGGAAAGGTAGAGGTTGTC
AAGTCATTGCAGTGGCCCGAACCTGTAACTTGATCCTGATTGTTTTGGATGTCCTGAAACCCTTGGGACATAAGAAGATA
ATTGAAAATGAACTGGAAGGCTTTGGCACTCGCTTGAACAGCAAACTCCCCAACATTGGCTTTAAGAAGGACAAGGGAGA
CATTAATCTCACAGCCACTTGCCCCCAGAGTGAGCTGGATACTGAAACTGTGAAAAGCATTCTGGCTGAATACAAGATTC
TTAATGCCAATGTGACTCTATGTAGTGATGCTACAGCTGATGACCTCATTGATGTGGTGGAAGGAAACAGTTTATAT

Alignment

ORF - retro_cjac_1104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.83 %
• Parental protein coverage: 65.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSTLAKIAEIEAEMARTQKNKATAHHLGLLKARLAKLRRELITPKGGGGGGPGEGFDVAKTGDARIGFV
          MSSTLAKI.EIEAEMARTQKNKATA.HL.LLK..LA.LR.ELITPKGGGGG.PGEGFDVAKTGDARIGFV
Retrocopy MSSTLAKIMEIEAEMARTQKNKATAYHLELLKGGLAELRQELITPKGGGGGSPGEGFDVAKTGDARIGFV

Parental  GFPSVGKSTLLSNLAGVYSEVAAYEFTTLTTVPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVAR
          GFPS.GKSTLLSNLAGVYSEVAAYEF.TLTT.PGVIRYKGAKIQLLDLPGIIEGAKDGKGRG.QVIAVAR
Retrocopy GFPSAGKSTLLSNLAGVYSEVAAYEFATLTTMPGVIRYKGAKIQLLDLPGIIEGAKDGKGRGCQVIAVAR

Parental  TCNLILIVLDVLKPLGHKKIIENELEGFGIRLNSKPPNIGFKKKDKGGINLTATCPQSELDAETVKSILA
          TCNLILIVLDVLKPLGHKKIIENELEGFG.RLNSK.PNIGF.KKDKG.INLTATCPQSELD.ETVKSILA
Retrocopy TCNLILIVLDVLKPLGHKKIIENELEGFGTRLNSKLPNIGF-KKDKGDINLTATCPQSELDTETVKSILA

Parental  EYKIHNADVTLRSDATADDLIDVVEGNRVY
          EYKI.NA.VTL.SDATADDLIDVVEGN..Y
Retrocopy EYKILNANVTLCSDATADDLIDVVEGNSLY

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	12.89 RPM
SRP051959_heart	0.23 RPM	12.47 RPM
SRP051959_kidney	0.38 RPM	15.18 RPM
SRP051959_liver	0.15 RPM	12.93 RPM
SRP051959_lung	0.47 RPM	12.97 RPM
SRP051959_lymph_node	0.16 RPM	14.47 RPM
SRP051959_skeletal_muscle	0.04 RPM	17.67 RPM
SRP051959_spleen	0.25 RPM	15.90 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1104 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007040	1 retrocopy	retro_amel_1448,
Canis familiaris	ENSCAFG00000032601	6 retrocopies	retro_cfam_1535, retro_cfam_1807, retro_cfam_382, retro_cfam_415, retro_cfam_453, retro_cfam_607,
Ciona intestinalis	ENSCING00000003305	1 retrocopy	retro_cint_1,
Callithrix jacchus	ENSCJAG00000011009	4 retrocopies	retro_cjac_1104 , retro_cjac_2246, retro_cjac_2606, retro_cjac_855,
Cavia porcellus	ENSCPOG00000010791	1 retrocopy	retro_cpor_1401,
Ciona savignyi	ENSCSAVG00000006503	1 retrocopy	retro_csav_10,
Dasypus novemcinctus	ENSDNOG00000001312	1 retrocopy	retro_dnov_531,
Homo sapiens	ENSG00000185721	1 retrocopy	retro_hsap_2231,
Gorilla gorilla	ENSGGOG00000011185	1 retrocopy	retro_ggor_1665,
Myotis lucifugus	ENSMLUG00000007033	1 retrocopy	retro_mluc_1447,
Macaca mulatta	ENSMMUG00000019099	1 retrocopy	retro_mmul_999,
Mustela putorius furo	ENSMPUG00000012810	1 retrocopy	retro_mputfur_339,
Mus musculus	ENSMUSG00000020457	1 retrocopy	retro_mmus_2366,
Nomascus leucogenys	ENSNLEG00000027001	1 retrocopy	retro_nleu_2627,
Pan troglodytes	ENSPTRG00000014272	1 retrocopy	retro_ptro_1578,
Ictidomys tridecemlineatus	ENSSTOG00000014187	1 retrocopy	retro_itri_460,
Tarsius syrichta	ENSTSYG00000010160	3 retrocopies	retro_tsyr_1374, retro_tsyr_1918, retro_tsyr_405,