RetrogeneDB ID: retro_cjac_1067

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:1994717..1995333(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMRAL1
• Ensembl ID: ENSCJAG00000019832
• Aliases: None
• Description: NmrA-like family domain containing 1 [Source:HGNC Symbol;Acc:24987]

Sequence

>retro_cjac_1067
GGAAAGCTGCTAGCTGATCTGGCCAACCGCCTGGGCCTCCACCATGTGGTCTACAGTGGCCTGGAGAACATCAAGAAGCT
GACGGCTGGGAGACTGACCGCCGCGCACCTTGACCGCAAAGGGGAGGTGTAGGGATATTTCCAGGACATCGGTGTTCCCA
CGACCAGTGTGCGGCTGCCCTGCTGTTTCGAGAACGTCCTCTCCCACTTCCTGCCCCAGAAAGCCCCGGACAGAAAGAGC
TACTTGCTAAGCTTGACCGCAGGTGACGTTCCCATGGGTGGCATGTCCGCGTCCGACCTGGGTCCCGTGGTGCTCAGCCT
GCTGAAGATACCAGAAAAATATGTCGGCCAGAGCATCAGGCTGAGCACTTGTAGACAACGGTCGAGGCGTACGCTGCTCT
GCTCACCAGGCACGCCCCGAGGTCGTGCACGGCACCAAGATGACTCCTGAGGACTCCGAAAGGCTCGGCTTCCCCGGGGC
CCAGGACCTGGCAGACATGTTCCCTTTCTATGCCCTGAGACCCGACTGTGACATCGAGCTGACCCTGACACTCAACCCCA
AGGCCCTAACGCTGGACTGGTGGCTGGAACAGCACAAAGGGGACTTGGCCCTGCTG

Alignment

ORF - retro_cjac_1067 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.21 %
• Parental protein coverage: 68.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKLLADLAKRLGLHYVVYSGLENIKKLTAGRLTAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENFLSHF
          GKLLADLA.RLGLH.VVYSGLENIKKLTAGRLTAAH.D.KGEV..YF.DIGVP.TSVRLPC.FEN.LSHF
Retrocopy GKLLADLANRLGLHHVVYSGLENIKKLTAGRLTAAHLDRKGEV*GYFQDIGVPTTSVRLPCCFENVLSHF

Parental  LPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRH-TAEEYAALLTKHT
          LPQKAPD.KSYLLSL..GDVPM.GMS.SDLGPVVLSLLK.PEKYVGQ.I.LSTCR..T.E.YAALLT.H.
Retrocopy LPQKAPDRKSYLLSLTAGDVPMGGMSASDLGPVVLSLLKIPEKYVGQSIRLSTCRQ<TVEAYAALLTRHA

Parental  RK-VVHNTKMTPEDYEKLGFPGAQDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFVLL
          ...VVH.TKMTPED.E.LGFPGAQDLA.MF.FYALRPD.DIELTL.LNPKALTLD.WLEQHKGD..LL
Retrocopy PR<VVHGTKMTPEDSERLGFPGAQDLADMFPFYALRPDCDIELTLTLNPKALTLDWWLEQHKGDLALL

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	1.42 RPM
SRP051959_heart	0.00 RPM	5.68 RPM
SRP051959_kidney	0.00 RPM	4.13 RPM
SRP051959_liver	0.00 RPM	4.44 RPM
SRP051959_lung	0.00 RPM	4.47 RPM
SRP051959_lymph_node	0.00 RPM	5.71 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.74 RPM
SRP051959_spleen	0.00 RPM	5.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1067 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1067 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1067 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
Ailuropoda melanoleuca	ENSAMEG00000001876	1 retrocopy	retro_amel_804,
Callithrix jacchus	ENSCJAG00000019832	1 retrocopy	retro_cjac_1067 ,