RetrogeneDB ID: retro_cjac_3930

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286302.1:21698..22378(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RND2
• Ensembl ID: ENSCJAG00000013018
• Aliases: None
• Description: Rho family GTPase 2 [Source:HGNC Symbol;Acc:18315]

Sequence

>retro_cjac_3930
GTGGAGGGGCAGAGCGGCCGCTGCAAGATCGTGGTGGTGGGAGATGCGGAGTGCGGCAAGACGGCGCTGCTGCAGGTGTT
CGCCAAGGACGCCTTTCCCGGGAGTTATGTCCCCACCGTGCTTGAGAACTACACCGAGAGCTTTGAGATCGACAAGTGCC
GCATTGAGCGCAACATGTGGGACACTTCAGGTTCCTCTTACTATGATAATGTCCGGCCTCTGGCCTATCCTGATTCTGAC
GCTGTGCTCATCTGCTTCGACATTAGCCGACCAGAAACACTGGACAGTGTTCTCAGGAAGTGGCAAGGAGAGACTCAAGA
GTTTTGCCCCAATGCCAAGGTTGTGCTGGTTGGCTGTTAACTAGACATGCGGACTGACCTGGGCACACTGAGGGAGCTGT
CCAAGCAGAGGCTTATCCCTGTCACACATGAGCAGGGCACTGTGCTAGCCAAGCAGGTGGGGGCTGTGTCCTACGTGGAT
GCTCCTCCCGGTCCTCTGAGCGCAGCGTCAGGGATGTCTTCCATGTGGCCACAGTGGCCTACCTTGGCCGTGGTCATAGG
CAGCTGCGCCGAACTGACTCACGCCAGGGAATGCAGCGATCCACTTAGCTGTCAGGACGGCTAGACCGAGAGAATGAGGG
CGACATACATAAGGATCGAGCCAAGAGCTGCAACCTCATG

Alignment

ORF - retro_cjac_3930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEGQSGRCKIVVVGDAECGKTALLQVFAKDAYPGSYVPTVFENYTASFEIDKRRIELNMWDTSGSSYYDN
          .EGQSGRCKIVVVGDAECGKTALLQVFAKDA.PGSYVPTV.ENYT.SFEIDK.RIE.NMWDTSGSSYYDN
Retrocopy VEGQSGRCKIVVVGDAECGKTALLQVFAKDAFPGSYVPTVLENYTESFEIDKCRIERNMWDTSGSSYYDN

Parental  VRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNAKVVLVGCKLDMRTDLATLRELSKQRLIP
          VRPLAYPDSDAVLICFDISRPETLDSVL.KWQGETQEFCPNAKVVLVGC.LDMRTDL.TLRELSKQRLIP
Retrocopy VRPLAYPDSDAVLICFDISRPETLDSVLRKWQGETQEFCPNAKVVLVGC*LDMRTDLGTLRELSKQRLIP

Parental  VTHEQGTVLAKQVGAVSYVE-CSSRSSERSVRDVFHVATVASLGRGHRQLRRTDSRRGMLRSTQLSGRPD
          VTHEQGTVLAKQVGAVSYV..CSSRSSERSVRDVFHVATVA.LGRGHRQLRRTDSR.GM.RST.LSGR.D
Retrocopy VTHEQGTVLAKQVGAVSYVD<CSSRSSERSVRDVFHVATVAYLGRGHRQLRRTDSRQGMQRST*LSGRLD

Parental  RGNEGEIHKDRAKSCNLM
          R.NEG.IHKDRAKSCNLM
Retrocopy RENEGDIHKDRAKSCNLM

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	1.04 RPM
SRP051959_heart	0.00 RPM	0.09 RPM
SRP051959_kidney	0.00 RPM	0.53 RPM
SRP051959_liver	0.00 RPM	0.22 RPM
SRP051959_lung	0.03 RPM	0.28 RPM
SRP051959_lymph_node	0.00 RPM	0.98 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.17 RPM
SRP051959_spleen	0.00 RPM	1.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3930 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3930 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3930 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Callithrix jacchus	ENSCJAG00000013018	1 retrocopy	retro_cjac_3930 ,
Callithrix jacchus	ENSCJAG00000013657	2 retrocopies	retro_cjac_1657, retro_cjac_2027,
Myotis lucifugus	ENSMLUG00000004129	4 retrocopies	retro_mluc_1125, retro_mluc_1356, retro_mluc_2145, retro_mluc_459,
Mus musculus	ENSMUSG00000001313	1 retrocopy	retro_mmus_3087,