RetrogeneDB ID: retro_cjac_2382

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:140289971..140290331(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032766
• Aliases: None
• Description: None

Sequence

>retro_cjac_2382
CATCTTCCACAAAGGACAACTTTGGAGAGCAGTCGTAGCCAAAACCTCCCTCTGCCTTTAAGAAGTCTCAGAACTCCAGG
CTACATATCATCTTCTTCATGGGAAAGATGTGGAATTTCCCAGGAACTATCCATCAGGTTGTCTTCTGGGCTGTCTGGAC
CTAACTGGTTGTTTCAGAAGCAATTTAAGGAGCAGTTTCCAGACGTCAGTCAAGAATCACGTTCTCCACTTGTTTTCATC
TCCAAAAATCCTCAGGAAATGGTTGTGGAGTTTCCTATTAAAGAAAATAAAAAAATCTGGAAACTGGATTCCAAGATCCA
CCAAGGAGCAAAGAAGGGGTAAATGAAGCAGAATACAGCT

Alignment

ORF - retro_cjac_2382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.85 %
• Parental protein coverage: 93.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YTPHRGRLWIAATAKKPSPQ-EVSELQATYRLLRGKDVEFPNDYPSGCLLGCVDLIDCLSQKQFKEQF-P
          ..P.R..L........P.P..EVSELQATY.LL.GKDVEFP..YPSGCLLGC.DL..C.........F.P
Retrocopy HLPQRTTLESSRSQNLPLPL>EVSELQATYHLLHGKDVEFPRNYPSGCLLGCLDLTGCF-RSNLRSSF<P

Parental  DVSQESDSPFVFICKNPQEMVVKFPVKGNPKIWKLDSKIHQGAKKGLMKQNKA
          DVSQES.SP.VFI.KNPQEMVV.FP.K.N.KIWKLDSKIHQGAKKG.MKQN.A
Retrocopy DVSQESRSPLVFISKNPQEMVVEFPIKENKKIWKLDSKIHQGAKKG*MKQNTA

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	3.57 RPM
SRP051959_heart	0.02 RPM	3.21 RPM
SRP051959_kidney	1.69 RPM	2.57 RPM
SRP051959_liver	0.06 RPM	1.84 RPM
SRP051959_lung	0.00 RPM	3.66 RPM
SRP051959_lymph_node	0.00 RPM	4.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.95 RPM
SRP051959_spleen	0.00 RPM	3.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2382 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2382 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032766	1 retrocopy	retro_cjac_2382 ,
Macaca mulatta	ENSMMUG00000009882	1 retrocopy	retro_mmul_1853,
Oryctolagus cuniculus	ENSOCUG00000002322	1 retrocopy	retro_ocun_663,