RetrogeneDB ID: retro_cjac_437

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82216905..82217385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002838
• Aliases: None
• Description: None

Sequence

>retro_cjac_437
ATGGAGGACGTCTTGGCCGGGCCCCTGCACAGGGCGGCGGCGGAGGCGGCCGAGGCGTGAGCGCGGCCCGGGGTGACGCT
GCTGCCCTTAGCGCCCCTCTCAGGGACTGCGGAGGCGGACGAGGGCGGCGGCCACTGGAGCTTCATTGACTGCGAGATGG
AGGAGGCGGACCTGCAGGACCTGCCCAGCGCCACCATCGCCTGCCACCCGGACCCGCCCGTGTTTGTGGACGGCCTGTGC
CGGGCCAAATTTGAGTTTCTCTTTAGGACATAAGGCAAGGACATCGCTTTTCAGTATTTTAAGAGTTTCAAAAGAGTCAG
AATAAACTTCAGCAACCCCTTCTCCGCAGCAGATGTCAGGCTCCAGCTGCATAAGACTGAGTTTCTGGGAAAGGAAATGA
AGTTACATTTTGCTCAGACCTTACACATAGGAAGCTCACACCTGGCTCCGCCAAACCCCGACAAGCAGTTTCTGATCTCC

Alignment

ORF - retro_cjac_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.75 %
• Parental protein coverage: 64.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDGLAGPRHGAAAEATEARARPGATLRPFAPLSGTAEADEGGGDWSFIDCEMEEVDLQDLPSATIACHL
          MED.LAGP.H.AAAEA.EA.ARPG.TL.P.APLSGTAEADEGGG.WSFIDCEMEE.DLQDLPSATIACH.
Retrocopy MEDVLAGPLHRAAAEAAEA*ARPGVTLLPLAPLSGTAEADEGGGHWSFIDCEMEEADLQDLPSATIACHP

Parental  DPRVFVDGLCRAKFESLFRTYDKDITFQYFKSFKRVRINFSNPFSAADARLQLHKTEFLGKEMKLYFAQT
          DP.VFVDGLCRAKFE.LFRT..KDI.FQYFKSFKRVRINFSNPFSAAD.RLQLHKTEFLGKEMKL.FAQT
Retrocopy DPPVFVDGLCRAKFEFLFRT*GKDIAFQYFKSFKRVRINFSNPFSAADVRLQLHKTEFLGKEMKLHFAQT

Parental  LHIGSSHLAPPNPDKQFLIS
          LHIGSSHLAPPNPDKQFLIS
Retrocopy LHIGSSHLAPPNPDKQFLIS

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	12.60 RPM
SRP051959_heart	0.05 RPM	31.59 RPM
SRP051959_kidney	0.35 RPM	110.18 RPM
SRP051959_liver	0.06 RPM	29.11 RPM
SRP051959_lung	0.02 RPM	14.32 RPM
SRP051959_lymph_node	0.00 RPM	10.96 RPM
SRP051959_skeletal_muscle	0.00 RPM	78.01 RPM
SRP051959_spleen	0.00 RPM	14.12 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_437 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_437 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002838	2 retrocopies	retro_cjac_4016, retro_cjac_437 ,
Callithrix jacchus	ENSCJAG00000012084	1 retrocopy	retro_cjac_2149,
Cavia porcellus	ENSCPOG00000010683	1 retrocopy	retro_cpor_1267,
Tarsius syrichta	ENSTSYG00000006972	1 retrocopy	retro_tsyr_1913,