RetrogeneDB ID: retro_cjac_3868

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285434.1:26435..26798(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HINT3
• Ensembl ID: ENSCJAG00000003710
• Aliases: None
• Description: histidine triad nucleotide binding protein 3 [Source:HGNC Symbol;Acc:18468]

Sequence

>retro_cjac_3868
ATGGCAGATGAACGGGTGAGCAGCGCCGACCTGGCCACCGACTGTAAGGCCCCGGAGACTACAGAGTCTACGGCTTCCTC
GGTGGGGTCCTGCGAAGCCGCCACCAAGTCACCGGAGCCCAAGGACAATGACAGCACCTGCGTGTTCCGCGGGATCGCAG
GGCGGCAGGTCCCGGGCACCGAACTCCTGCACTGCGAGAATGAGGACCTGGTTTGCTTCAGAAATATCAAACCAGCAGCA
ACTCATCATTATCTTATGGTGCCAAAGAAGCATACTGGAAATTGCAGATCTCTAAGGAAAGAGCAAGTAGAACTGGCTGA
GAACATAGTAACTGTTGGAAAAACCATTCTTAGGAATAATTTC

Alignment

ORF - retro_cjac_3868 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 67.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADEQVNRSAGLAPDFKAPETTECTASSVGTCEAAAKSPEPKDNDSTCVFCRIAGRQDPGTELLHCENED
          MADE.V..SA.LA.D.KAPETTE.TASSVG.CEAA.KSPEPKDNDSTCVF..IAGRQ.PGTELLHCENED
Retrocopy MADERVS-SADLATDCKAPETTESTASSVGSCEAATKSPEPKDNDSTCVFRGIAGRQVPGTELLHCENED

Parental  LVCFKDIKPAATHHYLVVPKKHIGNCRSLRKDQVELVENMVTVGKTILERNNF
          LVCF..IKPAATHHYL.VPKKH.GNCRSLRK.QVEL.EN.VTVGKTIL.RNNF
Retrocopy LVCFRNIKPAATHHYLMVPKKHTGNCRSLRKEQVELAENIVTVGKTIL-RNNF

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	0.35 RPM	8.61 RPM
SRP051959_heart	0.19 RPM	15.77 RPM
SRP051959_kidney	0.38 RPM	32.41 RPM
SRP051959_liver	0.19 RPM	18.37 RPM
SRP051959_lung	0.37 RPM	11.01 RPM
SRP051959_lymph_node	0.46 RPM	6.76 RPM
SRP051959_skeletal_muscle	0.09 RPM	18.47 RPM
SRP051959_spleen	0.50 RPM	7.56 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3868 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3868 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001830	1 retrocopy	retro_chof_38,
Callithrix jacchus	ENSCJAG00000003710	1 retrocopy	retro_cjac_3868 ,
Cavia porcellus	ENSCPOG00000021856	1 retrocopy	retro_cpor_674,
Echinops telfairi	ENSETEG00000007350	1 retrocopy	retro_etel_1567,
Macropus eugenii	ENSMEUG00000007627	1 retrocopy	retro_meug_853,
Mus musculus	ENSMUSG00000019791	1 retrocopy	retro_mmus_1387,