RetrogeneDB ID: retro_cjac_583

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:87171046..87171901(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FBXO6
• Ensembl ID: ENSCJAG00000013250
• Aliases: None
• Description: F-box protein 6 [Source:HGNC Symbol;Acc:13585]

Sequence

>retro_cjac_583
ATGGATGCTCCCCACCCCACCGCAGCCCTGGCCAGCATTAACGAGCTGCCAGAGAACATCCCGCTGGAGCTGTTATTGCA
CGTGCCCGCCCGCCAGCTGCTGCTGAACTGCCGCCCCGTCTGCAGCCTCTGGCGGGACCTCATTGACCTCATGATCCTCT
GGAAGAGCAAGTGTCTGCGAGACGGCTTCATCCCCAAGGACTGGGACCAGCCTGTGGAGGACTGGAAGATCTGCTACTTC
CTAAGGAGCCTGCAGAGCAACCTCCTGCACGACCCATGTGCCGAAGAAGGTATGTTAGCATGGCAAATCATTACCAAAGG
TGGCGACAACTGGAAGGTGGAGAGCCTCCCTGGAGCCCATGGGACAGATTTTCCTGACCACAAAGTCAAGAAGTATTTTG
TCACGTCTTACGAGATGTGCCTCAAGTCCCAGCTGGTGGACCTTGTAGCCAAGGGCTACTGGAAGGAGCTACTGGACACG
TTCAGGCCAGACATCACAGTTAAGGACTAGTTTGCCGCCAGAGCCGACTGTGGCTGCACCTACCAACTCAACGTGTACCT
GGCCTCGGCTGACTACTTCGTGTTGGATTCCTTCGAGCCCCCACCTGTGACCATTGAACAGTGGAACGATGCCGCATGGA
CAGAGTTCTCCCACACCTTCTCGGACTACCCTCCAGGTGTCTGCTACATCCCCTTCGGGCACGGGGGCCAGGACACCCAG
TACTGGGCAGGCTGGTACGGGCCCCGAGTCACTAACAGCAGCATCGCTGTCAGCCACAAGATGACCAGGAACCCGGCCTC
CTCCGAGGCTCAGCCTGGGCAGACCCAATCGCCCTACAAAGTTGTTCTCCCAATC

Alignment

ORF - retro_cjac_583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDAPHPTTALASINELPENILLELFLHVPARQLLLNCRPVCSLWRDLIDLMILWKRKCLRDGFITKDWDQ
          MDAPHPT.ALASINELPENI.LEL.LHVPARQLLLNCRPVCSLWRDLIDLMILWK.KCLRDGFI.KDWDQ
Retrocopy MDAPHPTAALASINELPENIPLELLLHVPARQLLLNCRPVCSLWRDLIDLMILWKSKCLRDGFIPKDWDQ

Parental  PVEDWKICYFLRSLQRNLLRNPCAEEGMLAWQIDTEGGDKWKVESLPGAHRTAFPDPKVKNYFVTSYGMC
          PVEDWKICYFLRSLQ.NLL..PCAEEGMLAWQI.T.GGD.WKVESLPGAH.T.FPD.KVK.YFVTSY.MC
Retrocopy PVEDWKICYFLRSLQSNLLHDPCAEEGMLAWQIITKGGDNWKVESLPGAHGTDFPDHKVKKYFVTSYEMC

Parental  LKSQLVDLVAKGYWEELLDTFRPDIVVKDWFAARHDCGCTYQLKVYLASADYFVLDSFEPPPVTINQWSD
          LKSQLVDLVAKGYW.ELLDTFRPDI.VKD.FAAR.DCGCTYQL.VYLASADYFVLDSFEPPPVTI.QW.D
Retrocopy LKSQLVDLVAKGYWKELLDTFRPDITVKD*FAARADCGCTYQLNVYLASADYFVLDSFEPPPVTIEQWND

Parental  ATWTEVSHTFSDYPPGVRYILFRHGGQDTQFWAGWYGPGVTNSSIVVSHKMSRNLASSEAQPGQTQLPYK
          A.WTE.SHTFSDYPPGV.YI.F.HGGQDTQ.WAGWYGP.VTNSSI.VSHKM.RN.ASSEAQPGQTQ.PYK
Retrocopy AAWTEFSHTFSDYPPGVCYIPFGHGGQDTQYWAGWYGPRVTNSSIAVSHKMTRNPASSEAQPGQTQSPYK

Parental  VVLPI
          VVLPI
Retrocopy VVLPI

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	10.76 RPM
SRP051959_heart	0.00 RPM	8.03 RPM
SRP051959_kidney	0.00 RPM	6.63 RPM
SRP051959_liver	0.00 RPM	6.28 RPM
SRP051959_lung	0.02 RPM	5.69 RPM
SRP051959_lymph_node	0.00 RPM	5.41 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.31 RPM
SRP051959_spleen	0.02 RPM	5.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_583 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_583 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_583 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013250	1 retrocopy	retro_cjac_583 ,
Myotis lucifugus	ENSMLUG00000006843	1 retrocopy	retro_mluc_928,