RetrogeneDB ID: retro_cjac_424

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:77485304..77486370(+)
• Located in intron of: ENSCJAG00000031617

Retrocopy information

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

Parental gene information

• Parental gene symbol: FEZF2
• Ensembl ID: ENSCJAG00000019670
• Aliases: None
• Description: None

Sequence

>retro_cjac_424
AGCGGCCTCCGGGCGGGCGGTGGCGGTGGCCGCGGCGGCGTGGGGCCCAGTGTGCGGCGCCAGCGGCTTGTGCAAAACCA
ACTGTGGCTTGTGCTGCAAGGCCGAGCTGGGCCTGGCGCCCACTGCGCTGCCCGCGGGCAGGGTCATCAAGCCGCAGGTC
ATCAACCAGGCCATGGGACTGCTGGCCAGCGGCTCGGTCTACTATTTCAACTACCTGGACTCGACCGCGTACCCACTGTC
TGAGCTCCTCAGCAGCGACCTCTTCCCTTCTGGCCTCCTCAATGTGCAGGCCCCGCCGCACTGGCTGCTCACCCCAAGCT
CTTTCTGCTGGAAAACGCCAAGCTGGCCCGCCTGACTGCAGACAAGTTCCCCCATCTGGCTCCCTACCCCCATAAGTAGC
GCTTGACGGCGCCGCTGGAGCAGGTACTGAAGGAGAACTCAGCCCTGACTGCCAAACGCAGAGGCGTTAAGGGCCACAGC
AAGCTGCCAGGGGCTCCACAGACGGCAAGCCCAAAAACTTCACCTGCGAGGTGTGTGGCAAGGTGTTTAATGCTCACTAT
AACCTCACCTGCCACATGCCGGTCCACACCGGAGCCAGACCGTTCGTGTGCCAAGTCTGTGGCAAAGGCTTTTGCCAGGC
CAGCACGCTCTGCAGGCACAAAATTATACACACTCAGGAAAAGCCGCATAAATGCAACCAGTGTGGCAAAGCGTTCAACC
GCAGCTCCACGCTCAACATGCATATCCTCATCCACGCGGGCTACAAGCCCTTCGTCTGCGAATTTTGTGGCAAAGGCTTT
CACCAAAAAGGGAACTGCAAGAACCACAAACTGACCACAGTGGCCAGAAGCAGTACAAATATACCATCAGCAACAACGCC
TTCCACCAGGTCTACAACCTGACCTTCCATATGCACACCCACAATGACAAGAAGCCTTTCACGTGCGCCACTTGCGGCAA
AGGGTTTTGCAGAAACGTTGACTTAAAGAAACATGTGCGCAAACTCCACGACAGCGTGGGCCCTGCTGCCCCCTCCACAA
CGGACCTGACTAGGACAGTGCAGAGC

Alignment

ORF - retro_cjac_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 77.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SGGGGGGGGGGGG-GAPVCGASGLCKTNCGVCCKAELGLAPSALPAGRVIKPQVINQAVGLPASGSLYYF
          SG...GGGGG.GG...PVCGASGLCKTNCG.CCKAELGLAP.ALPAGRVIKPQVINQA.GL.ASGS.YYF
Retrocopy SGLRAGGGGGRGG>WGPVCGASGLCKTNCGLCCKAELGLAPTALPAGRVIKPQVINQAMGLLASGSVYYF

Parental  NYLDSTAYPPSELLSGHLFPSGLLNAQAP-AALAAHPKLFLLENAKLAGLAADKFPHPAPYPHKERLPAP
          NYLDSTAYP.SELLS..LFPSGLLN.QAP.AALAAHPKLFLLENAKLA.L.ADKFPH.APYPHK.RL.AP
Retrocopy NYLDSTAYPLSELLSSDLFPSGLLNVQAP<AALAAHPKLFLLENAKLARLTADKFPHLAPYPHK*RLTAP

Parental  LEQVLKENSALTAERGGVKGHSKLPG-GSADGKPKNFTCEVCGKVFNAHYNLTRHMPVHTGARPFVCKVC
          LEQVLKENSALTA.R.GVKGHSKLPG.GS.DGKPKNFTCEVCGKVFNAHYNLT.HMPVHTGARPFVC.VC
Retrocopy LEQVLKENSALTAKRRGVKGHSKLPG<GSTDGKPKNFTCEVCGKVFNAHYNLTCHMPVHTGARPFVCQVC

Parental  GKGFRQASTLCRHKIIHTQEKPHKCNQCGKAFNRSSTLNTHIRIHAGYKPFVCEFCGKGFHQKGNYKNHK
          GKGF.QASTLCRHKIIHTQEKPHKCNQCGKAFNRSSTLN.HI.IHAGYKPFVCEFCGKGFHQKGN.KNHK
Retrocopy GKGFCQASTLCRHKIIHTQEKPHKCNQCGKAFNRSSTLNMHILIHAGYKPFVCEFCGKGFHQKGNCKNHK

Parental  LT-HSGEKQYKCTICNKAFHQVYNLTFHMHTHNDKKPFTCATCGKGFCRNFDLKKHVRKLHDSVGPAAPS
          LT.HSG.KQYK.TI.N.AFHQVYNLTFHMHTHNDKKPFTCATCGKGFCRN.DLKKHVRKLHDSVGPAAPS
Retrocopy LT<HSGQKQYKYTISNNAFHQVYNLTFHMHTHNDKKPFTCATCGKGFCRNVDLKKHVRKLHDSVGPAAPS

Parental  AKDLTRTVQS
          ..DLTRTVQS
Retrocopy TTDLTRTVQS

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	0.16 RPM	0.00 RPM
SRP051959_heart	0.32 RPM	0.00 RPM
SRP051959_kidney	0.33 RPM	0.02 RPM
SRP051959_liver	0.17 RPM	0.00 RPM
SRP051959_lung	0.36 RPM	0.02 RPM
SRP051959_lymph_node	0.50 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.09 RPM	0.00 RPM
SRP051959_spleen	0.29 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_424 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019670	1 retrocopy	retro_cjac_424 ,