RetrogeneDB ID: retro_cjac_2449

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:71725142..71725915(-)
• Located in intron of: ENSCJAG00000009988

Retrocopy information

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

Parental gene information

• Parental gene symbol: NECAP2
• Ensembl ID: ENSCJAG00000008146
• Aliases: None
• Description: NECAP endocytosis associated 2 [Source:HGNC Symbol;Acc:25528]

Sequence

>retro_cjac_2449
ATGACAGAGAGCGGGTATGAGTCGGTGCTCTGTGTCAAGCCTGACGTCCACGTCTACCGCATTCCCAACCATGGCTACAG
GGCCCCGAGTGGCAGCTGGACCAGCCATCATGGAGTGGCCGGCTGAGGATCACTGCAAAGCGGCAGATGGCCTGCATCAA
GCTGGGGGACAGGTCTCAGGGGAGCTCTTTGCTGCGGCCCCAGTGGATCAGCTTCCTGGCACAGCTGTGGAGAGCATGAG
GGATCCCAGCAAGTACGTCGTGACCCACATTGAAGGTGGAGACCGGTGACGGACGTTTATTGGAATTGGCCTTGGGGACT
GAGGTGATGCCTTTGACTTCAATGTTGCATTGCAGGATCATTTCAAGTGGGTGAAACAGCAGTGTGAATTTGCAAAAAAA
GCCCAGAACCCAGACCAAGGCCCCAAATTGGACCTGGGCTTCGAGGAGGGCCAGACCATCAGGCTCAACAGCGCAAACAT
GAAGAAGGAGGAAGGAGCGGCCGGGAATCCCTGAGCCCGTCCTGCCAGCACGGGAGGGTTGTGCTTGCTTCCCCCTCCCC
CAGGGGGCAAAACTTTCACCCTCATCCCTCCCCCCAGGGAACAGTTGTCAGTCGGGGGAATCCCTTGTCCAACCAGCAGT
TGCTCCCAGTTCAGGAGGAGGTGCTTCTGTACCCTGGCCACAGCCCAAGCCTGCCACCACTGACATCTGGGGAGACTTTA
CCAAATCTACAGGATCAGCTCCCAGCCAGACCCAACCAGGCTGGGTCCAGTTC

Alignment

ORF - retro_cjac_2449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MEESGYESVLCVKPDVHVYRIPPRATNRGYRAA-EWQLDQPSWSGRLRITAKGQMAYIKLEDRT-SGELF
          M.ESGYESVLCVKPDVHVYRIP....N.GYRA..EWQLDQPSWSGRLRITAK.QMA.IKL.DR..SGELF
Retrocopy MTESGYESVLCVKPDVHVYRIP----NHGYRAP<EWQLDQPSWSGRLRITAKRQMACIKLGDRS<SGELF

Parental  AQAPVDQFPGTAVESVTDSSRYFVIRIEDGNGRRAFIGIGFGDRGDAFDFNVALQDHFKWVKQQCEFAKQ
          A.APVDQ.PGTAVES..D.S.Y.V..IE.G...R.FIGIG.GD.GDAFDFNVALQDHFKWVKQQCEFAK.
Retrocopy AAAPVDQLPGTAVESMRDPSKYVVTHIEGGDR*RTFIGIGLGD*GDAFDFNVALQDHFKWVKQQCEFAKK

Parental  AQNPDQSPKLDLGFKEGQTIKLNIANMKKKEGAAGNPRARPASTGGLSLLPPPPGGRTSTLIPPPGEQLS
          AQNPDQ.PKLDLGF.EGQTI.LN.ANMKK.EGAAGNP.ARPASTGGL.LLPPPPGG.T.TLIPPP.EQLS
Retrocopy AQNPDQGPKLDLGFEEGQTIRLNSANMKKEEGAAGNP*ARPASTGGLCLLPPPPGGKTFTLIPPPREQLS

Parental  VGG-SLVQPAVAPTS-GGASVPWPQPKPATAATADIWGDFTKSTGSTSSQTQPGWVQF
          VGG.SLVQPAVAP.S.GGASVPWPQPKPAT....DIWGDFTKSTGS..SQTQPGWVQF
Retrocopy VGG>SLVQPAVAPSSGGGASVPWPQPKPAT---TDIWGDFTKSTGSAPSQTQPGWVQF

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	0.13 RPM	12.20 RPM
SRP051959_heart	0.04 RPM	8.61 RPM
SRP051959_kidney	0.11 RPM	15.51 RPM
SRP051959_liver	0.06 RPM	9.68 RPM
SRP051959_lung	0.28 RPM	19.07 RPM
SRP051959_lymph_node	0.23 RPM	32.94 RPM
SRP051959_skeletal_muscle	0.17 RPM	4.04 RPM
SRP051959_spleen	0.36 RPM	34.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2449 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2449 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
Canis familiaris	ENSCAFG00000015895	1 retrocopy	retro_cfam_1864,
Callithrix jacchus	ENSCJAG00000008146	2 retrocopies	retro_cjac_1447, retro_cjac_2449 ,
Macropus eugenii	ENSMEUG00000006140	1 retrocopy	retro_meug_2149,