RetrogeneDB ID: retro_cjac_1945

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:108567621..108568326(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009558
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1945
ATGGAGTTCGTCAAGTGCCTAGGCCACCCGGAGGAGTTCTACAACCTGGTGCGCCTCCGCATTGGGAGCAAGCGGAAGGT
GATGCCCAAGATGGACCAGGACTCGCTCAGCAGCAGCCTGAAAACTCGCTACACGTATCTGAATCAGACGAGTTGCAGTT
TCGCAGCTGTTATCCAGGTGCTGGATGGGGAAATGTGCAATGCAGTGTGCATATTTTATCTGGTCCTCCGAGCTCTGGAC
ATGCTGGAAGATGACATGACCATCAGTGTGGAAAAGAAGGTCCCGCTGTTACACAACGTCCACTTCCACTCTTTCCTTTA
CCAGCCAGACTGGCGGTTCATGGAGAGCAAGGAGAAGGACAGCCAGGTGCTGGAAGACTTCCCAACGATCTCCCTCGAGT
TTAGAAATTTGGCTGAGAAATACCAAACGGTGATCGCTGACATTTGCCGGAGAATGGGAACTGGGATGGCAGAGTTTTTG
AATAAGCATGTGACCTCTGAACAGGAGTGGGACAAGTACTGCCACTATGTTGCTGGGCTGGGAGGAATTGGCCTTTCCCG
TCTCTTCTCGGCCTCAGAGTTCGAAGACTCCTTAGTTGGTGAAGATACAGAACGTGCCAACTCCATGGGCTTGTTTCTGC
AGAAGACAAACATCATTTGTGACTATCTGGAAGACCAGCAAGAAGGAAGAGAGTTTTGGCCTCGA

Alignment

ORF - retro_cjac_1945 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.19 %
• Parental protein coverage: 55.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFVKCLGHPEEFYNLVRFRIGGKRKVMPKMDQDSLSSSLKTCYTYLNQTSRSFAAVIQALDGEMRNAVC
          MEFVKCLGHPEEFYNLVR.RIG.KRKVMPKMDQDSLSSSLKT.YTYLNQTS.SFAAVIQ.LDGEM.NAVC
Retrocopy MEFVKCLGHPEEFYNLVRLRIGSKRKVMPKMDQDSLSSSLKTRYTYLNQTSCSFAAVIQVLDGEMCNAVC

Parental  IFYLVLRALDTLEDDMTISVEKKVPLLHN--FHSFLYQPDWRFTESKEKDRQVLEDFPTISLEFRNLAEK
          IFYLVLRALD.LEDDMTISVEKKVPLLHN..FHSFLYQPDWRF.ESKEKD.QVLEDFPTISLEFRNLAEK
Retrocopy IFYLVLRALDMLEDDMTISVEKKVPLLHNVHFHSFLYQPDWRFMESKEKDSQVLEDFPTISLEFRNLAEK

Parental  YQTVIADICRRMGIGMAEFLNKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMG
          YQTVIADICRRMG.GMAEFLNKHVTSEQEWDKYCHYVAGL.GIGLSRLFSASEFED.LVGEDTERANSMG
Retrocopy YQTVIADICRRMGTGMAEFLNKHVTSEQEWDKYCHYVAGLGGIGLSRLFSASEFEDSLVGEDTERANSMG

Parental  LFLQKTNIIRDYLEDQQEGREFWPQ
          LFLQKTNII.DYLEDQQEGREFWP.
Retrocopy LFLQKTNIICDYLEDQQEGREFWPR

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	0.00 RPM	25.20 RPM
SRP051959_heart	0.00 RPM	14.73 RPM
SRP051959_kidney	0.00 RPM	14.51 RPM
SRP051959_liver	0.00 RPM	88.59 RPM
SRP051959_lung	0.00 RPM	11.83 RPM
SRP051959_lymph_node	0.00 RPM	12.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	34.96 RPM
SRP051959_spleen	0.00 RPM	7.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1945 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1945 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1945 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,