RetrogeneDB ID: retro_cjac_2645

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:99021242..99021567(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZSWIM7
• Ensembl ID: ENSCJAG00000012208
• Aliases: None
• Description: zinc finger, SWIM-type containing 7 [Source:HGNC Symbol;Acc:26993]

Sequence

>retro_cjac_2645
GAATATCAGTTATCGCTGAAGCTTCTCTTTGGCTCATCAGCCACTCAGGCCTTGGACCTAGTTGATCGACAATCCATAAC
CTTAATCTCATCGCCCAGTGGAAGGCATGTTTACCAGGTACTTGGAAGTTATAGGAAAACATACACGTTTGGCTTCTTGT
TCATGTCCTGTATTTGCCTTCCCAGTGCTACGGAAGAGTGACAGCATCCTGTGCAGGCATCTCTTGGCAGTTTACCTTAG
TTAGGTTTTGAGCGCCTGTCAGCAGCTAAGTGTCTCCAACAAGCAGTTGACTGACATATTATTGATGGAGAAGAAACAAG
AACCA

Alignment

ORF - retro_cjac_2645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.3 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYLLSLKFLFGSSATQALDLVDRQSITLIASPSGRRVYQVLGSS-GKTYTCLASCHYCSCPAFAFKVLRK
          EY.LSLK.LFGSSATQALDLVDRQSITLI.SPSGR.VYQVLGS..GK..T.LAS...CSCP.FAF.VLRK
Retrocopy EYQLSLKLLFGSSATQALDLVDRQSITLISSPSGRHVYQVLGSY>GK-HTRLAS---CSCPVFAFPVLRK

Parental  SDSILCKHLLAVYLSQVMRTCQQLSVSDKQLTDILLMEKKQEP
          SDSILC.HLLAVYLS.V...CQQLSVS.KQLTDILLMEKKQEP
Retrocopy SDSILCRHLLAVYLS*VLSACQQLSVSNKQLTDILLMEKKQEP

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	0.18 RPM	5.57 RPM
SRP051959_heart	0.05 RPM	6.54 RPM
SRP051959_kidney	0.04 RPM	6.37 RPM
SRP051959_liver	0.02 RPM	7.41 RPM
SRP051959_lung	0.13 RPM	3.89 RPM
SRP051959_lymph_node	0.00 RPM	4.04 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.62 RPM
SRP051959_spleen	0.06 RPM	4.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2645 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2645 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2645 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012208	1 retrocopy	retro_cjac_2645 ,