RetrogeneDB ID: retro_cjac_2400

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:2722664..2723099(-)
• Located in intron of: ENSCJAG00000010717

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRAS
• Ensembl ID: ENSCJAG00000036517
• Aliases: None
• Description: neuroblastoma RAS viral (v-ras) oncogene homolog [Source:HGNC Symbol;Acc:7989]

Sequence

>retro_cjac_2400
TTTGCAGATGAATATGATCCCACCATAGAGGATTCTTAGAGAAAACAGGTGGTTTCAGATGGTGAAACCCGTCTGCTGAA
CACTCTCCATACAGCTAGACAAGAAGAGTCCAGTGCCATGAGAGACCAATACATGGGGACAGGCGAAGGCTTCCTCTGCG
CCCTTACCAACAATAACAGCAAGTCATTTGTGGATATTAATCTCTACAGGGAGCAGATTAAGCAAGTGAAGGACTCAGAT
TATGTACCTCTGGTGCTAGCGGGAAGCAAGTGTGATATGCCAACAAGTACAGTTGATACAAAACAAGGCCACAAACTGGC
CAAGAGTTACAGTATTCCACTGACTAAAACCTCAGCCAAGACCAGACAGGCTGTTGAAGATGCTCTTTACACACTGCTAA
GGGAAGTACACCAGTACCAAATGAAAAACCTCAAC

Alignment

ORF - retro_cjac_2400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 76.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYR
          F.DEYDPTIEDS.RKQVV.DGET.LL..L.TA.QEE.SAMRDQYM.TGEGFLC....NNSKSF.DINLYR
Retrocopy FADEYDPTIEDS*RKQVVSDGETRLLNTLHTARQEESSAMRDQYMGTGEGFLCALTNNNSKSFVDINLYR

Parental  EQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYR
          EQIK.VKDSD.VP.VL.G.KCD.PT.TVDTKQ.H.LAKSY.IP...TSAKTRQ.VEDA.YTL.RE..QY.
Retrocopy EQIKQVKDSDYVPLVLAGSKCDMPTSTVDTKQGHKLAKSYSIPLTKTSAKTRQAVEDALYTLLREVHQYQ

Parental  MKKLH
          MK.L.
Retrocopy MKNLN

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	1.09 RPM	27.65 RPM
SRP051959_heart	0.74 RPM	26.71 RPM
SRP051959_kidney	0.89 RPM	29.57 RPM
SRP051959_liver	0.11 RPM	18.91 RPM
SRP051959_lung	1.40 RPM	29.90 RPM
SRP051959_lymph_node	0.14 RPM	28.67 RPM
SRP051959_skeletal_muscle	0.09 RPM	45.64 RPM
SRP051959_spleen	0.48 RPM	27.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2400 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2400 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2400 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400 ,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,