RetrogeneDB ID: retro_cjac_407

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:70700610..70701372(+)
• Located in intron of: ENSCJAG00000033311

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOXN3
• Ensembl ID: ENSCJAG00000017620
• Aliases: None
• Description: None

Sequence

>retro_cjac_407
GTGGACAAGGAGAGGAGTCAGAGTCGTTGTGGTGGAAAAGGGTCGTTGTGGTGCATAGACCCACAGTATAGATAAAACTT
AATTCAGGCTTTGAAAAAGACACCTTATAACCCACACCCACACGTGTTTAATACACCTCCCACCTGTCCTCAGGCATATC
AAAGCACATCAGGTCCACCCATATGGCCGGGCAGTACCTTCTTCAAGAGAAACGGAGCCCTTCTCCAAGTTCCTCCAGAA
GTGATCCAAAATGGAGCGCGAGTCCTGAGCCGAAGGCTGTTTCCTGGCGTGTGGCCGCTGCCCATCACTCCCACTGGGGT
GACAGCGGCCATGAGGAACGGCATCACCAGCTGCTGGATATGGACTGAGATCGAGCCGTCGTGCTGCTCCCCCGTGGTCA
GCAGAGACCCCAACGAGGATCACAACTACAGCAGTGCCAAGTCCTCCAATGTCCCGAGCACCTCTCCCACCAGCGACTCC
ATCTCCTCCTCTTCCTCCTCCTCCTCCTCCTCCGACCACTACGAGTTTGCCACCAAGAGGAGCCAGGAGGGCAGCGAGGG
GAGATGCTGGAGCCACGAGAGCCACAGTGACACTGAAGAAAACGACAGGAAGCACAGCCAAAAGGAGCCCAAGGATGCTC
TGGGGGACAGTGGGTATGCATCCCAGCACAAGAAGCGCCAGCACTTCGCCAAGGCCAGAAGGGTCCCCAGCGACACACTG
CCCCTCAAAAAGAGACGCACCGAAAAGCCCCCCGAGAGCGAC

Alignment

ORF - retro_cjac_407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.16 %
• Parental protein coverage: 54.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDKERSQSI--GKGSLWCIDPEYRQNLIQALKKTPYHPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR
          VDKERSQS...GKGSLWCIDP.YR.NLIQALKKTPY.PHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR
Retrocopy VDKERSQSRCGGKGSLWCIDPQYR*NLIQALKKTPYNPHPHVFNTPPTCPQAYQSTSGPPIWPGSTFFKR

Parental  NGALLQVPPGVIQNGARVLSRGLFPGVRPLPITPIGVTAAMRNGITSCRMRTESEPSCGSPVVSGDPKED
          NGALLQVPP.VIQNGARVLSR.LFPGV.PLPITP.GVTAAMRNGITSC...TE.EPSC.SPVVS.DP.ED
Retrocopy NGALLQVPPEVIQNGARVLSRRLFPGVWPLPITPTGVTAAMRNGITSCWIWTEIEPSCCSPVVSRDPNED

Parental  HNY-SSAKSSNVRSTSPTSDSISSSSSSSADDHYEFATKGSQEGSEGSEGSFRSHESHSDTEEDDRKHSQ
          HNY.S...S......................DHYEFATK.SQ...EGSEG...SHESHSDTEE.DRKHSQ
Retrocopy HNYSSAKSSNVPSTSPTSDSXXXXXXXXXXXDHYEFATKRSQ---EGSEGRCWSHESHSDTEENDRKHSQ

Parental  KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD
          KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD
Retrocopy KEPKDALGDSGYASQHKKRQHFAKARRVPSDTLPLKKRRTEKPPESD

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	13.53 RPM
SRP051959_heart	0.00 RPM	37.80 RPM
SRP051959_kidney	0.00 RPM	14.22 RPM
SRP051959_liver	0.00 RPM	22.05 RPM
SRP051959_lung	0.00 RPM	26.04 RPM
SRP051959_lymph_node	0.00 RPM	21.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.80 RPM
SRP051959_spleen	0.00 RPM	37.08 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_407 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_407 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_407 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	ENSCJAG00000017620	1 retrocopy	retro_cjac_407 ,
Nomascus leucogenys	ENSNLEG00000016989	1 retrocopy	retro_nleu_2677,