RetrogeneDB ID: retro_cjac_2709

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:28944473..28945312(+)
• Located in intron of: ENSCJAG00000011038

Retrocopy information

• Ensembl ID: ENSCJAG00000019664
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: XRCC2
• Ensembl ID: ENSCJAG00000032080
• Aliases: None
• Description: X-ray repair complementing defective repair in Chinese hamster cells 2 [Source:HGNC Symbol;Acc:12829]

Sequence

>retro_cjac_2709
ATGTGTAGTGACTTCCATAGGGCTGAGTCTGGGACCGAGCTCCTTGCCCGACTTGAAGGTAGAAGTTCTTTGAAAGAAAT
AGAACCAAGTCTGTTTGCTGATGAAGATTCTCCTGTGCATGGTGATATTCTTGAATTTCATGGCCCAGAAGAACAGGAAA
AACAGAAATGCTTTATCATTTAACAGCACGATGTATACTTCCCAAATCAGAAGGAGGCCTGGAAGTAGAAGTCGTATTTA
TCGATACAGATTATCACTTTGATATGCTCCGGCTCGTGACGATCCTCGAGCACAGACTGTCCCAGAGCTCTGAGGAAGTG
CTCAAGGTCTGCCTGGGGAGACTGGTGCTGCTGTACTGCAGCAGCAGCACCCACTTACTGCTCATGCTTCACTCACTGGA
GAGCATGTTTTGTAGTCGCCCGTCTCTTTGCCTTTTGATTTTGGATAGCCTGTCAGCTTTTTACTGGATAGATCGCGTCA
ACGGAGGAGAAAGTGTTAACTTACAGGAGTCTACTCTGAAGAAATGTTCTCAGTTCTTAGAGAAACTTGTAAATGACTAT
CGCCTGGTTCTTTTTGCAACCACACAAACTTTAATGCAGAAAGCCTCGAACTCGGTGGAAGAACCTTCTCATGCCTCCCA
ACGCCTGCGTGACGTGGACATAGACTATAGACCCTATCTCTGTAAAGCATGGCAGCAAGTGGTGAAGCACAGGATATTTT
TCTCCAAACAAGATGATTCGAAAAGCAGAAACCAATTTTCATTAGTTTCACGCTGTTTAAAAAGTAAGAATGTAAAAAAA
CACTTTTTTATTATTGGAGAAAGTGGGGTTGAATTTTGT

Alignment

ORF - retro_cjac_2709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MCSDFHRAESGTELLARLEGRSSLKEIEPSLFADEDSPVHGDILEFHGPEG-TGKTEMLYHLTARCILPK
          MCSDFHRAESGTELLARLEGRSSLKEIEPSLFADEDSPVHGDILEFHGPE..TGKTEMLYHLTARCILPK
Retrocopy MCSDFHRAESGTELLARLEGRSSLKEIEPSLFADEDSPVHGDILEFHGPEE<TGKTEMLYHLTARCILPK

Parental  SEGGLEVEVVFIDTDYHFDMLRLVTILEHRLSQSSEEVLKVCLGRLVLLYCSSSTHLLLTLHSLESMFCS
          SEGGLEVEVVFIDTDYHFDMLRLVTILEHRLSQSSEEVLKVCLGRLVLLYCSSSTHLLL.LHSLESMFCS
Retrocopy SEGGLEVEVVFIDTDYHFDMLRLVTILEHRLSQSSEEVLKVCLGRLVLLYCSSSTHLLLMLHSLESMFCS

Parental  RPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLKKCSQFLEKLVNDYRLVLFATTQTLMQKASNSVEEP
          RPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLKKCSQFLEKLVNDYRLVLFATTQTLMQKASNSVEEP
Retrocopy RPSLCLLILDSLSAFYWIDRVNGGESVNLQESTLKKCSQFLEKLVNDYRLVLFATTQTLMQKASNSVEEP

Parental  SHASQRLRDMDIYYRPYLCKAWQQVVKHRIFFSKQDDSKSRNQFSLVSRCLKSKSVKKHFFIIGESGVEF
          SHASQRLRD.DI.YRPYLCKAWQQVVKHRIFFSKQDDSKSRNQFSLVSRCLKSK.VKKHFFIIGESGVEF
Retrocopy SHASQRLRDVDIDYRPYLCKAWQQVVKHRIFFSKQDDSKSRNQFSLVSRCLKSKNVKKHFFIIGESGVEF

Parental  C
          C
Retrocopy C

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	2.02 RPM	1.31 RPM
SRP051959_heart	1.12 RPM	1.23 RPM
SRP051959_kidney	1.60 RPM	1.18 RPM
SRP051959_liver	0.80 RPM	0.69 RPM
SRP051959_lung	1.37 RPM	1.46 RPM
SRP051959_lymph_node	1.74 RPM	2.08 RPM
SRP051959_skeletal_muscle	0.72 RPM	0.35 RPM
SRP051959_spleen	1.58 RPM	1.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2709 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2709 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	ENSCJAG00000032080	1 retrocopy	retro_cjac_2709 ,