RetrogeneDB ID: retro_cjac_3908

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286226.1:103235..103699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020356
• Aliases: None
• Description: None

Sequence

>retro_cjac_3908
GCTCTAATCATTCTTTCAGAAAGTCAAAGTGCTGATGAGGAAGAAGAAGAAAAAGGGCCAGTGCCCCCAGGAATCTGCAG
GAGTCTGTGGAGGAGGAAGCCCCCTAGGGGTCCAGGGATGGAGGTTATTCAATTCTCTCAATTCTCCTGGCACATTTGCC
TTCAATGAGCCTTACAGGAGTAACTTGCACTCATTCAAGGAACAGCAAGTCAACTTGGCTTATGACATAGGCAAGATTAA
AAAGGACCAACAAGAGGAAGAATACCAAGGCCCACTGTGCCCCAGGCTCAGCATGGAGCTGGTGGAAGCAGAAGAGCCTG
AAGTCTTCTGGTACTCACTGGATATATTTTATTCAACATATGTGGCTTATCCTGAGTTTTATTACACATACCAGGCTTAC
ACATATGCCATTTTTTTTATTTGTAGAAGAGCATGTTCACTTGACTTTGGACATGAACTGTAGG

Alignment

ORF - retro_cjac_3908 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.22 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLNLFTESQSDDEEEEEKGPV-STRNLQESVEEEAPQESWDEDYSTLSI-PPGTFAFNEPYRTNLHSLEE
          .L....ESQS.DEEEEEKGPV...RNLQESVEEEAP..S.D..YS.LSI..PGTFAFNEPYR.NLHS..E
Retrocopy ALIILSESQSADEEEEEKGPV<APRNLQESVEEEAP*GSRDGGYSILSI<SPGTFAFNEPYRSNLHSFKE

Parental  QQVNLAHDIDKIEKDQEEEEDQGPLCPRLSMELVEAEEPEVFWYSLDILYSTYTAYLEFYYTCQAYTYAV
          QQVNLA.DI.KI.KDQ.EEE.QGPLCPRLSMELVEAEEPEVFWYSLDI.YSTY.AY.EFYYT.QAYTYA.
Retrocopy QQVNLAYDIGKIKKDQQEEEYQGPLCPRLSMELVEAEEPEVFWYSLDIFYSTYVAYPEFYYTYQAYTYAI

Parental  -FLYAEEHVRLTLDMDSR
          .FL..EEHV.LTLDM..R
Retrocopy >FLFVEEHVHLTLDMNCR

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	0.02 RPM
SRP051959_heart	0.00 RPM	0.23 RPM
SRP051959_kidney	0.02 RPM	0.33 RPM
SRP051959_liver	0.00 RPM	0.13 RPM
SRP051959_lung	0.00 RPM	0.41 RPM
SRP051959_lymph_node	0.00 RPM	0.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.00 RPM	0.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3908 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3908 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3908 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	ENSCJAG00000020356	1 retrocopy	retro_cjac_3908 ,