RetrogeneDB ID: retro_cjac_1781

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:42246185..42246816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NKX6-1
• Ensembl ID: ENSCJAG00000005335
• Aliases: None
• Description: NK6 homeobox 1 [Source:HGNC Symbol;Acc:7839]

Sequence

>retro_cjac_1781
GCAGGGCTGCTGGCCAGACTGCCCCGTTTCAGCAGCCTGAGCCCGCCGCCACCGCCGCCCGGGCTCTACTTCAGCCCCAG
CGCTGCTGCCGTGGCCGCCGTGGGCCGGTACCCCAAGCCGCTAGCGGAGCTGCCCAGCCGGATGCCCATCTTCTGGCCCG
AAGTGATGCGGAGGCTGCCCTGAAGGGATGCACGCCTAGCCTGTACCCCTCATCAAGGATCCATGTTGTTGGACAAAGAC
GGGAAGAAAAAACACACACAACCCACTTTTTCCGGACTTTATTCACCCTGGAGAAGACTTTCGAACAAACAATACTTGGC
GGGGTCCGAGAGGGCTCGCTTGGCCTATTCGTTGGGGATGACGGAAAGTCAGGCCAAGGTCTGGTTCCAGAACCGCCGGA
CCAAGTGGAGGAAGAAGCACGCAGCCGAGATGGCCACGGCCAAGAAGCAGCAGGACTCGGAGACCAAGAGGCTCAATGGG
GGCCTCGGAGAAGAAGGAGGAGGACGACGACTACAAGCCTCTAGATCCCAACTCGGACGACGAGAAAATCACGCAGCTGC
TGAAGAAGCACAAGTCCAGCAGCAGCGGCGGTGGCCTCCTACTGCGCGCGTCCGAGCCCGAGAGCTCATCC

Alignment

ORF - retro_cjac_1781 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 58.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGLLAGLPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELPGRTPIFWPGVMQSPPWRDARLACTP
          AGLLA.LPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELP.R.PIFWP.VM...P.RDARLACTP
Retrocopy AGLLARLPRFSSLSPPPPPPGLYFSPSAAAVAAVGRYPKPLAELPSRMPIFWPEVMRRLP*RDARLACTP

Parental  HQGSILLDKDGKRKHTRPTFSGQQIFALEKTFEQTKYLAGPERARLAYSLGMTESQVKVWFQNRRTKWRK
          HQGS.LLDKDGK.KHT.PTFSG..............YLAG.ERARLAYSLGMTESQ.KVWFQNRRTKWRK
Retrocopy HQGSMLLDKDGKKKHTQPTFSG--LYSPWRRLSNKQYLAGSERARLAYSLGMTESQAKVWFQNRRTKWRK

Parental  KHAAEMATAKKKQDSETERLK-GASENEEEDDDYNKPLDPNSDDEKITQLLKKHKSSSGGGGLLLHASEP
          KHAAEMATAKK.QDSET.RL..GASE..EEDDDY.KPLDPNSDDEKITQLLKKHKSSS.GGGLLL.ASEP
Retrocopy KHAAEMATAKKQQDSETKRLN>GASEKKEEDDDY-KPLDPNSDDEKITQLLKKHKSSSSGGGLLLRASEP

Parental  ESSS
          ESSS
Retrocopy ESSS

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.02 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1781 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1781 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1781 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	ENSCJAG00000005335	1 retrocopy	retro_cjac_1781 ,