RetrogeneDB ID: retro_cjac_3959

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286435.1:152091..152694(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D4
• Ensembl ID: ENSCJAG00000018601
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 4 [Source:HGNC Symbol;Acc:28998]

Sequence

>retro_cjac_3959
ATGCACTCGGATGCCGCCGCTGTCAACTTTCAGCTGAACTCCCATCTCTCAACACTGGCAAATATTCATAAGATCTACCA
CACCTTTAATAAGCTAAACCTAACAGAAGACGATGACCAAGACGATCACCAAACAGGAAGTCTGCGGTCTTGCAGTTCTT
CAGACTGCTTTAATAAAGTGATGCCACCAAGGAAAAAGGGAAGACCCGCCTCTGGAGATGATTTATCTGTCAAGAAAAGT
AGACATGATAGCATGTATAGAAAATATGATTCAACTAGAATAAAGACTGAAGAAGAAACCTTTTCAAATAAAAGGTTCTA
TGAATATGCAGGCACTGATGATGTTGTAGGCCCTGAAGGCATGGAGAAATTTTGTGAAGACATTGGTGTTGAACCAGAAA
ACGTAGTTATGCTTGTCCTGGCTTGGAAATTGGATGCACAAAACATGGGCTATTTTACTCTACAAGAGTGGTTAAAAGGA
ATGACTTCTCTCCAATGTGACACAACAGAAAAACTCAGAAATACTTTGGATTACTTAAGATCATTATTAAATGATTCTAC
AAACTTTAAACTTATTTACAGATATGCGTTTGACTTTGCACGG

Alignment

ORF - retro_cjac_3959 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.63 %
• Parental protein coverage: 79.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHSDAAAVNFQLNSHLSTLANIHKIYHTLNKLNLTEDVGQDDHQTGSLRSCSSSDCFNKVMPPRKKRRPA
          MHSDAAAVNFQLNSHLSTLANIHKIYHT.NKLNLTED..QDDHQTGSLRSCSSSDCFNKVMPPRKK.RPA
Retrocopy MHSDAAAVNFQLNSHLSTLANIHKIYHTFNKLNLTEDDDQDDHQTGSLRSCSSSDCFNKVMPPRKKGRPA

Parental  SGDDLSAKKSRHDSMYRKYDSTRIKTEEEAFSSKRCLEWFYEYAGTDDVVGPEGMEKFCEDIGVEPENVV
          SGDDLS.KKSRHDSMYRKYDSTRIKTEEE.FS.KR....FYEYAGTDDVVGPEGMEKFCEDIGVEPENVV
Retrocopy SGDDLSVKKSRHDSMYRKYDSTRIKTEEETFSNKR----FYEYAGTDDVVGPEGMEKFCEDIGVEPENVV

Parental  MLVLAWKLDAQNMGYFTLQEWLKGMTSLQCDTTEKLRNTLDYLRSLLNDSTNFKLIYRYAFDFAR
          MLVLAWKLDAQNMGYFTLQEWLKGMTSLQCDTTEKLRNTLDYLRSLLNDSTNFKLIYRYAFDFAR
Retrocopy MLVLAWKLDAQNMGYFTLQEWLKGMTSLQCDTTEKLRNTLDYLRSLLNDSTNFKLIYRYAFDFAR

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	13.16 RPM
SRP051959_heart	0.09 RPM	25.10 RPM
SRP051959_kidney	0.07 RPM	21.59 RPM
SRP051959_liver	0.13 RPM	13.54 RPM
SRP051959_lung	0.11 RPM	18.61 RPM
SRP051959_lymph_node	0.16 RPM	19.84 RPM
SRP051959_skeletal_muscle	0.04 RPM	10.74 RPM
SRP051959_spleen	0.08 RPM	20.21 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3959 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3959 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3959 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Callithrix jacchus	ENSCJAG00000018601	1 retrocopy	retro_cjac_3959 ,
Cavia porcellus	ENSCPOG00000008945	2 retrocopies	retro_cpor_1176, retro_cpor_1179,
Sarcophilus harrisii	ENSSHAG00000017879	1 retrocopy	retro_shar_437,