RetrogeneDB ID: retro_cjac_2811

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:52174835..52175537(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51
• Ensembl ID: ENSCJAG00000020821
• Aliases: None
• Description: RAD51 recombinase [Source:HGNC Symbol;Acc:9817]

Sequence

>retro_cjac_2811
ATGGCAATGCAGATGCAGATTGAAGCAAATGCAGATACTTCAGTGGAAGAAGAAAGCTTTGGCCCACAACCTGTTTCACG
GTTAGAGCAGTGTGGCATAAATGCCAATGATGTGAAAAAATTGGAAGAAGCTGGATTCCATACTGTGGAGGCTGTTGCCT
ATGCACCAAAGAAGGAGCTAATAAATATTAAGGGAATTAGTGAAGCCAAAGCTGATAAAATTCTGGCTGAAGCAGCCAAA
TTAGTTCCAATGGGTTTCACCGCTGCAACTGAATTCCACCAAAGGCGGTCAGAGATCATACAGATTACTACTGGCTCTAA
AGAGCTTGACAAACTACTTCAAGGTGGAATTGAGACTGGCTCTATCACAGAAATGTTTGGAGAATTCCGAACTGGGAAGA
CCCAGATCTGTCATACACTGGCTGTCACCTGCCAGCTTCCCATTGACCGGGGCAGAGGTGTAGGAAAGGCCATGTACATT
GACACCAAGGGTACCTTTAGGCCAGAACGGCTGCTAGCAGTGGCTGAGAGGTATGGTCTCTCTGGTAGTGATGTCCTGGA
TAATGTAGCATATGCTCGAGCATTCAACACAGACCACCAGACCCAGCTCCTTTAGCAAGCATCAGCCATGATGGTAGAAT
CTAGGTATGCACTGCTTATTGTAGACAGTGCCACCGCCCTTTACAGAACAGACTACTCGGGC

Alignment

ORF - retro_cjac_2811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.15 %
• Parental protein coverage: 68.93 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMQMQLEANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK
          MAMQMQ.EANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK
Retrocopy MAMQMQIEANADTSVEEESFGPQPVSRLEQCGINANDVKKLEEAGFHTVEAVAYAPKKELINIKGISEAK

Parental  ADKILAEAAKLVPMGFTTATEFHQRRSEIIQIT-GCKELDNLLQGGIETGSITEMFGEFRTGKTQICHTL
          ADKILAEAAKLVPMGFT.ATEFHQRRSEIIQIT.G.KELD.LLQGGIETGSITEMFGEFRTGKTQICHTL
Retrocopy ADKILAEAAKLVPMGFTAATEFHQRRSEIIQITTGSKELDKLLQGGIETGSITEMFGEFRTGKTQICHTL

Parental  AVTCQLPIDRGGGEGKAMYIDTEGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLLYQASAM
          AVTCQLPIDRG.G.GKAMYIDT.GTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLL.QASAM
Retrocopy AVTCQLPIDRGRGVGKAMYIDTKGTFRPERLLAVAERYGLSGSDVLDNVAYARAFNTDHQTQLL*QASAM

Parental  MVESRYALLIVDSATALYRTDYSG
          MVESRYALLIVDSATALYRTDYSG
Retrocopy MVESRYALLIVDSATALYRTDYSG

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	0.60 RPM	2.53 RPM
SRP051959_heart	0.02 RPM	0.32 RPM
SRP051959_kidney	0.02 RPM	0.27 RPM
SRP051959_liver	0.09 RPM	0.37 RPM
SRP051959_lung	0.08 RPM	0.59 RPM
SRP051959_lymph_node	0.32 RPM	1.14 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.20 RPM
SRP051959_spleen	0.08 RPM	1.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2811 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2811 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020821	2 retrocopies	retro_cjac_2811 , retro_cjac_430,
Ornithorhynchus anatinus	ENSOANG00000028534	1 retrocopy	retro_oana_26,
Otolemur garnettii	ENSOGAG00000031397	1 retrocopy	retro_ogar_3425,