RetrogeneDB ID: retro_cjac_4169

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:57312989..57313544(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51L1
• Ensembl ID: ENSCJAG00000015123
• Aliases: None
• Description: None

Sequence

>retro_cjac_4169
GCTTACGGGATAAAAGCACAGAGGTCTGCTGATTTCTCACCAGCATTCTTTTCTACTACCCTTTCTGCTTTGGATGAAGC
CCTGCATGCAGGTGTGGCTTGTGGATCCCTCACAGAGATTACAGGTCCACCAGGTTGTGGAAAAACTCAGTTTTGTATAA
TGATGAGCATTTTAGCTACATTATCCACCAATATGGGAGGATTAGAAGGAGCTGTGGTGTACATTGACACAGAGTCAGCA
TTTAGTGCTGAAAGACTGGTTGAGATAGCAGAATCCCATTTTCCCAGATATTTTAACACTGAAGAAAAATTAGTTTTGGC
AAGTAGTAAAGTTCATCTTTATCAGGAGCTCACCTATGATGAAGTTTTACAAAGGATTGAATCTTTGGAAGAAGAAATTA
TCTCAAAAGGAATTAAACTTGTGATTATTGACTCTCTTGCTTCTGTGGTCAATAAAGAGTTTGATACACAACTTCCAGGC
AATCTCAAAGAAAGAAACAAATTCTTGGCAAGAGAAGCATCTTCCTTGAAGTATTTGGCTGAGGAGTTTTCAGTA

Alignment

ORF - retro_cjac_4169 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.97 %
• Parental protein coverage: 67.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYGIKTQRSADFSPAFLSTTLSALDEALHGGVACGSLTEITGPPGCGKTQFCIMMSILATLPTNMGGLEG
          AYGIK.QRSADFSPAF.STTLSALDEALH.GVACGSLTEITGPPGCGKTQFCIMMSILATL.TNMGGLEG
Retrocopy AYGIKAQRSADFSPAFFSTTLSALDEALHAGVACGSLTEITGPPGCGKTQFCIMMSILATLSTNMGGLEG

Parental  AVVYIDTESAFSAERLVEIAESRFPRYFNTEEKLLLTSSKVHLYRELTCDEVLQRIESLEEEIISKGVKL
          AVVYIDTESAFSAERLVEIAES.FPRYFNTEEKL.L.SSKVHLY.ELT.DEVLQRIESLEEEIISKG.KL
Retrocopy AVVYIDTESAFSAERLVEIAESHFPRYFNTEEKLVLASSKVHLYQELTYDEVLQRIESLEEEIISKGIKL

Parental  VIIDSVASVVRKEFDTQLPGNLKERNKFLAREASSLKYLAEEFSI
          VIIDS.ASVV.KEFDTQLPGNLKERNKFLAREASSLKYLAEEFS.
Retrocopy VIIDSLASVVNKEFDTQLPGNLKERNKFLAREASSLKYLAEEFSV

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	0.04 RPM	4.42 RPM
SRP051959_heart	0.05 RPM	2.95 RPM
SRP051959_kidney	0.02 RPM	4.97 RPM
SRP051959_liver	0.00 RPM	2.32 RPM
SRP051959_lung	0.02 RPM	5.01 RPM
SRP051959_lymph_node	0.02 RPM	8.24 RPM
SRP051959_skeletal_muscle	0.02 RPM	2.12 RPM
SRP051959_spleen	0.02 RPM	6.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4169 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4169 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4169 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015123	1 retrocopy	retro_cjac_4169 ,