RetrogeneDB ID: retro_cjac_2761

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:122884630..122885881(+)
• Located in intron of: ENSCJAG00000005991

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDFT1
• Ensembl ID: ENSCJAG00000003988
• Aliases: None
• Description: farnesyl-diphosphate farnesyltransferase 1 [Source:HGNC Symbol;Acc:3629]

Sequence

>retro_cjac_2761
ATGGAGTTCGTAAAGTGCCTAGGCCACCCCGAGGAGTTCTACAACCTGGTGCGCTTCCGCATCGGGGGCAAGCGGAAGGT
GATGCCCAAGATGGACCAGGACTCGCTCAGCAGCAGCCTGAAAACTTGCTTCACGTATCTGAATCAGACGAGTCGCAGTT
TCGCAGCTGTTAGCCAGGCGCTGGATGGGGAAATGCGCAATGCAGTGTGCATATTTTATCTGGTCCTCCGAGCTCTGGAC
ACGCTGGAAGATGACATGACCATCAGTGTGGAAAAGAAGGTCCCGCTGTTATACAACTTCCACTCTTTCCTTTACCAGAC
AGACTGGCGGTTCACGGAAAGCAAGGAGAAGGACCGCCAGGTGCTGGAGGACTTCCCAACGATCTCCCTCGAGTTTAGAA
ATCTGGCTGAGAAATACCAAATGGTGATCGCTGACATTTGCCGGAGAATGGGAATTGGGATGGCAGAGTTTTTGAATAAG
CATGTGACCTCTGAACAGGAGTGGGACAAGTACTGCCACTATGTTGCTGGGCTGGTAGGAATTGGCCTTTCCAGTCTCTT
CTCGGCCTCAGAGTTCGAAGACCCCTTAGTTGGTGAAGATACAGAACGTGCCAACTCCATGGGCCTGTTTCTGCAGAAAA
CAAACATCATTCGTGACTATCTGGAAGACCAGCAAGAAGGAAGAGAGTTTTGGCCTCAAGAGGTTTGGAGCAGGTATGTT
AAGAAGCTGGGGGATTTTGCCAAGCCGGAGAATATTGAGTTGGCCGTGCAGTGCCTGAATGAACTTATAACCAACGCGCT
GCACCACATCCCAGACGTCATCACCTACCTTTCGAGACTCAGAAACCAGAGCGTGTTTAACTTCTGTGCTATCCCACAGG
TGATGGCCATTGCCACTTTGGCTGCCTGTTACAATAACCAGCAGGTGTTCAGAGGGGTAGTGAAGATTCGGAAAGGGCAA
GCAGTGACCCTGATGATGGATGCCACCAACATGCCAGCTGTCAAAGCCATCATATATCAGTATATGGAAGAGATTTACCA
TAGAATCCCCGACTCAGACCCATCTTCCAGTAAAACGAGGCAGATCATCTCCACCATCCCGACGCAGAATCTTCCCAACT
GTCAGCTGATCTCCCGAAGCCACTACTCCCCCATCTACCTGTCCTTTGTCATGCTCTTGGCTGCCCTGAGCTTGCAGTAC
CTGACCACACTCTCCCAGGTCACGGAAGACTATGTTCAGACTGGAGAACAC

Alignment

ORF - retro_cjac_2761 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTCYTYLNQTSRSFAAVIQALDGEMRNAVC
          MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTC.TYLNQTSRSFAAV.QALDGEMRNAVC
Retrocopy MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTCFTYLNQTSRSFAAVSQALDGEMRNAVC

Parental  IFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFTESKEKDRQVLEDFPTISLEFRNLAEKYQ
          IFYLVLRALDTLEDDMTISVEKKVPLL.NFHSFLYQ.DWRFTESKEKDRQVLEDFPTISLEFRNLAEKYQ
Retrocopy IFYLVLRALDTLEDDMTISVEKKVPLLYNFHSFLYQTDWRFTESKEKDRQVLEDFPTISLEFRNLAEKYQ

Parental  TVIADICRRMGIGMAEFLNKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLF
          .VIADICRRMGIGMAEFLNKHVTSEQEWDKYCHYVAGLVGIGLS.LFSASEFEDPLVGEDTERANSMGLF
Retrocopy MVIADICRRMGIGMAEFLNKHVTSEQEWDKYCHYVAGLVGIGLSSLFSASEFEDPLVGEDTERANSMGLF

Parental  LQKTNIIRDYLEDQQEGREFWPQEVWSRYVKKLGDFAKPENIELAVQCLNELITNALHHIPDVITYLSRL
          LQKTNIIRDYLEDQQEGREFWPQEVWSRYVKKLGDFAKPENIELAVQCLNELITNALHHIPDVITYLSRL
Retrocopy LQKTNIIRDYLEDQQEGREFWPQEVWSRYVKKLGDFAKPENIELAVQCLNELITNALHHIPDVITYLSRL

Parental  RNQSVFNFCAIPQVMAIATLAACYNNQQVFRGVVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIP
          RNQSVFNFCAIPQVMAIATLAACYNNQQVFRGVVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIP
Retrocopy RNQSVFNFCAIPQVMAIATLAACYNNQQVFRGVVKIRKGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIP

Parental  DSDPSSSKTRQIISTIRTQNLPNCQLISRSHYSPIYLSFVMLLAALSLQYLTTLSQVTEDYVQTGEH
          DSDPSSSKTRQIISTI.TQNLPNCQLISRSHYSPIYLSFVMLLAALSLQYLTTLSQVTEDYVQTGEH
Retrocopy DSDPSSSKTRQIISTIPTQNLPNCQLISRSHYSPIYLSFVMLLAALSLQYLTTLSQVTEDYVQTGEH

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	0.04 RPM	25.20 RPM
SRP051959_heart	0.04 RPM	14.73 RPM
SRP051959_kidney	0.07 RPM	14.51 RPM
SRP051959_liver	0.30 RPM	88.59 RPM
SRP051959_lung	0.02 RPM	11.83 RPM
SRP051959_lymph_node	0.02 RPM	12.37 RPM
SRP051959_skeletal_muscle	0.07 RPM	34.96 RPM
SRP051959_spleen	0.02 RPM	7.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2761 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2761 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003988	2 retrocopies	retro_cjac_1945, retro_cjac_2761 ,
Erinaceus europaeus	ENSEEUG00000013655	1 retrocopy	retro_eeur_97,
Loxodonta africana	ENSLAFG00000007372	1 retrocopy	retro_lafr_772,
Mus musculus	ENSMUSG00000021273	1 retrocopy	retro_mmus_1182,
Vicugna pacos	ENSVPAG00000006183	1 retrocopy	retro_vpac_463,