RetrogeneDB ID: retro_cjac_1563

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:59754467..59754998(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSCJAG00000010760
• Aliases: None
• Description: None

Sequence

>retro_cjac_1563
ACTCTGGGTGTGGTTTGAAGTCTGGAGATAGTTGTATTTTTGCACAGCTTTCCAATATCCAGCTATGATTGGTACAAGAT
TTGGGAAGGCCTGACCTTGAGGTTTCATGGAGTGCTTGTCCTTGATGTTTTAGGCTTTGGCTTTAGTGACAAACTGTGAC
CACATCACTATTGCATATTTGAGCAGGCCAGCATTGTGGAAGCACTTCTGTGGCATCTTGGGCTCCAGAACCACAGGACC
AACATTTTATCTCATGACTGTGGAGACATTGTTGCTCAGGAGCTGCTCTACTAGTAGAAGCAGAATCAATCTGGTAGGCT
TACCATAAAGAGTATCTGTCTGTCAGATGGAGGTATCTTTTCTGAGTCTCATCGTCCACTCTTTCTCCAAAAGCTACTCA
AAGATGGAGGTGTGCTGTCACCCATCCTCATGTGGGTGATGAACTTCTTTGCATTCTCTCGAGGTCTCACCCCAGTCTTT
GGGCCATGTACTCGGCCCTCTGAGAGTGAGCTGTGGAATGGGACATGTGGG

Alignment

ORF - retro_cjac_1563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 52.84 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVGVVGSPEIVVLLHGFPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALL
          ..GVV.S.EIVV.LH.FP.SSYDWYKIWEGLTLRFH.V..LD.LGFGFSDK..PHHY.IFEQASIVEALL
Retrocopy TLGVV*SLEIVVFLHSFPISSYDWYKIWEGLTLRFHGVLVLDVLGFGFSDKL*PHHYCIFEQASIVEALL

Parental  RHLGLQNRRINLLSHDYGDIVAQELLYRYKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGVLS
          .HLGLQN.R.N.LSHD.GDIVAQELLY..KQN.SGRLTIKS.CLS.GGIF.E.HRPL.LQKLLKDGGVLS
Retrocopy WHLGLQNHRTNILSHDCGDIVAQELLY**KQNQSGRLTIKSICLSDGGIFSESHRPLFLQKLLKDGGVLS

Parental  PILTRLMNFFVFSRGLTPVFGPYTRPSESELWDMWAG
          PIL...MNFF.FSRGLTPVFGP.TRPSESELW....G
Retrocopy PILMWVMNFFAFSRGLTPVFGPCTRPSESELWNGTCG

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	3.59 RPM
SRP051959_heart	0.04 RPM	11.63 RPM
SRP051959_kidney	0.00 RPM	5.92 RPM
SRP051959_liver	0.00 RPM	30.39 RPM
SRP051959_lung	0.00 RPM	2.86 RPM
SRP051959_lymph_node	0.00 RPM	1.46 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.05 RPM
SRP051959_spleen	0.02 RPM	43.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1563 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1563 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1563 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563 , retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610,
Tupaia belangeri	ENSTBEG00000008404	2 retrocopies	retro_tbel_1480, retro_tbel_526,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,