RetrogeneDB ID: retro_cjac_1568

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 17:64133120..64134017(+)
• Located in intron of: ENSCJAG00000012094

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOVL5
• Ensembl ID: ENSCJAG00000011119
• Aliases: None
• Description: ELOVL fatty acid elongase 5 [Source:HGNC Symbol;Acc:21308]

Sequence

>retro_cjac_1568
ATGGAACATTTTGATGCATCACTTAGTACCTATTTCAAGGCATTGCTAGGCCCCCGAGATACCAGAGTAAAACGATGGTT
TCTACTGGACAATTATATACCTACATTTATCTGCTCTGTCATATATTTACTAATTGTATGGCTGAGACCAAAATACATGA
GGAATAAACAGTCATTCTCTTGCTGGGGGATTTTAGTGGTGTATAACCTTGGACTCATGCTGCTGTCTGTGTATATGTTC
TGTGAGTTAGTAACAGGAGTGTGGGAAGGCAAATACAACTTCTTCTGTCAGGGCACACGCACCACAGGAAAATCAGATAT
GAAGATTATCCGTGTCCTTTGGTGGTACTACTTCTCCAAACTCATAGAGTTTATGGACACCTTCTTCTTCATCCTGCGCA
AGAAAAACCACCAGATCACGATCCTGCACGTCTACCACCACACCTCAATGCTGAACATCTGGTGGTCTGTGATGAACTGG
GTTCCCTGTGGCCACTCTTATTTTGGTGCCACACTTAATAGCTTCATCCACGTCCTCATGTACTCGTACTATGGTTTGTC
GTCCATCCCTTCCATGCGCCCATACCTCTGGTGGAAGAAGTACATCACTCAGGGGCAGTTGCTTCAGTTTGTGCTGACAA
TCATCCAGACCAGCTGCGGGGTCATCTGGCCATGCACGTTCCCTCTTGGTTGGTTGTATTTCCAGATTGGATATATGATT
TCCCTGATTACTCTCTTCACAAACTTCTACATTCAGACCTACAACAAGGAGGCGGCCTCCCGAAGGAAAGACCACCTGAA
GGACCACCAGAATGGGTCCGTGGCTGCTGTGAATGGACACACCAAAAGCTTTTCACCCCTGGAAAACAATGTGAAGCCAA
GGAAGCTGCGGAAGGAT

Alignment

ORF - retro_cjac_1568 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEHFDASLSTYFKALLGPRDTRVKGWFLLDNYIPTFICSVIYLLIVWLGPKYMRNKQPFSCRGILVVYNL
          MEHFDASLSTYFKALLGPRDTRVK.WFLLDNYIPTFICSVIYLLIVWL.PKYMRNKQ.FSC.GILVVYNL
Retrocopy MEHFDASLSTYFKALLGPRDTRVKRWFLLDNYIPTFICSVIYLLIVWLRPKYMRNKQSFSCWGILVVYNL

Parental  GLTLLSLYMFCELVTGVWEGKYNFFCQGTRTAGESDMKIIRVLWWYYFSKLIEFMDTFFFILRKNNHQIT
          GL.LLS.YMFCELVTGVWEGKYNFFCQGTRT.G.SDMKIIRVLWWYYFSKLIEFMDTFFFILRK.NHQIT
Retrocopy GLMLLSVYMFCELVTGVWEGKYNFFCQGTRTTGKSDMKIIRVLWWYYFSKLIEFMDTFFFILRKKNHQIT

Parental  ILHVYHHTSMLNIWWFVMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSIPSMRPYLWWKKYITQGQLLQF
          ILHVYHHTSMLNIWW.VMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSIPSMRPYLWWKKYITQGQLLQF
Retrocopy ILHVYHHTSMLNIWWSVMNWVPCGHSYFGATLNSFIHVLMYSYYGLSSIPSMRPYLWWKKYITQGQLLQF

Parental  VLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLIALFTNFYIQTYNKKEASRRKDHLKDHQNGSVAAVNGH
          VLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLI.LFTNFYIQTYNK..ASRRKDHLKDHQNGSVAAVNGH
Retrocopy VLTIIQTSCGVIWPCTFPLGWLYFQIGYMISLITLFTNFYIQTYNKEAASRRKDHLKDHQNGSVAAVNGH

Parental  TNSFSPLENNVRPRKLRKD
          T.SFSPLENNV.PRKLRKD
Retrocopy TKSFSPLENNVKPRKLRKD

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	0.82 RPM	24.83 RPM
SRP051959_heart	0.86 RPM	34.01 RPM
SRP051959_kidney	0.64 RPM	37.94 RPM
SRP051959_liver	0.35 RPM	98.97 RPM
SRP051959_lung	0.91 RPM	67.07 RPM
SRP051959_lymph_node	0.98 RPM	45.84 RPM
SRP051959_skeletal_muscle	0.37 RPM	11.27 RPM
SRP051959_spleen	1.13 RPM	33.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1568 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011119	1 retrocopy	retro_cjac_1568 ,
Ictidomys tridecemlineatus	ENSSTOG00000015170	2 retrocopies	retro_itri_120, retro_itri_143,
Tarsius syrichta	ENSTSYG00000000707	1 retrocopy	retro_tsyr_229,