RetrogeneDB ID: retro_cjac_3946

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286373.1:649654..650176(+)
• Located in intron of: ENSCJAG00000002425

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020634
• Aliases: None
• Description: None

Sequence

>retro_cjac_3946
GAGTTCTGCAGCAAGGTAGGCGGGCGGCCAGCATGGCTGGGCGCGTCCAGGCGGCCGGGGCCCGGGATCCTAGCCTGCAC
CCTGCGTGGCCGCCCGCTCTCCTTCCTGCTGCAGGTGTACGCGCCGACGCCCAGCCGCGCCGACGCCTTCCACCGGGGCA
TCTTCCTTTTCTGGTGCCGCGAGCCGCCATGCTGTACCGGCCTGTGAGTTTTTAGGAATCAACTACCCAGGAAAAATGAT
TTTTATTCATATGAGCCACCTTCTGAGAATCCTCCCCCAGAAACCGAATCGGTGTGTCTCCAACTTAAGTCTAGTGCTCA
TCTATGCAGGGTTTGTGGCTGTTTAGGCCCCAAAACGTGCTCCAGATGCCACAAAGTGTACTATTGCAGCAAGGAGCATC
AGACCCTAGACTGGAGACTGGGACATAAGCAGGCTTGTGCACAACCAAATCATTTGGACCATATAATTCCAGACCACAAC
TTCCTTTTTCCAGAATTTGAAATTGTAATAGAAACAGAAGAT

Alignment

ORF - retro_cjac_3946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.23 %
• Parental protein coverage: 50.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QFPSKVGGRPAWLGASGLPGPGALACALCGRPLSFLLQVYAPLPGRADAFHRGIFLFCCREPPCCAGLRV
          .F.SKVGGRPAWLGAS..PGPG.LAC.L.GRPLSFLLQVYAP.P.RADAFHRGIFLF.CREPPCC.GL.V
Retrocopy EFCSKVGGRPAWLGASRRPGPGILACTLRGRPLSFLLQVYAPTPSRADAFHRGIFLFWCREPPCCTGL*V

Parental  FRNQLPRKNDFYSYEPPSENPSPETESVCLQLKSGAHLCRVCGCLGPKTCSRCHKVYYCSKEHQTLDWRL
          FRNQLPRKNDFYSYEPPSENP.PETESVCLQLKS.AHLCRVCGCLGPKTCSRCHKVYYCSKEHQTLDWRL
Retrocopy FRNQLPRKNDFYSYEPPSENPPPETESVCLQLKSSAHLCRVCGCLGPKTCSRCHKVYYCSKEHQTLDWRL

Parental  GHKQAYAQPDHLDHRIPDHNFLFPEFEIVIETED
          GHKQA.AQP.HLDH.IPDHNFLFPEFEIVIETED
Retrocopy GHKQACAQPNHLDHIIPDHNFLFPEFEIVIETED

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	0.02 RPM	9.63 RPM
SRP051959_heart	0.05 RPM	8.95 RPM
SRP051959_kidney	0.00 RPM	10.32 RPM
SRP051959_liver	0.00 RPM	12.24 RPM
SRP051959_lung	0.03 RPM	9.63 RPM
SRP051959_lymph_node	0.02 RPM	13.26 RPM
SRP051959_skeletal_muscle	0.02 RPM	10.07 RPM
SRP051959_spleen	0.00 RPM	10.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3946 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3946 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3946 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	ENSAMEG00000017075	2 retrocopies	retro_amel_1329, retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946 ,
Cavia porcellus	ENSCPOG00000002920	1 retrocopy	retro_cpor_168,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,
Ictidomys tridecemlineatus	ENSSTOG00000022768	2 retrocopies	retro_itri_1348, retro_itri_1635,