RetrogeneDB ID: retro_cjac_1069

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:6180597..6181430(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM23
• Ensembl ID: ENSCJAG00000008482
• Aliases: None
• Description: None

Sequence

>retro_cjac_1069
GAGCCAATTGATAATCTGAGTCCTGAGGAGCGTGATGCCCGCACAGTTTTCTGTACGCAGTTAGCTGCCGCATTAGGCCT
GAGACCTGGAGGACTTTTGCTCTGCTGTAGCAAGGTTCGTCATGTACGTGTCATCTCAGATCGGAACTGATGCATTCTAA
GGGCATTGCCTCTGTGGAATCTGTGAAATCCAATCTGTGCCACTGGCCATTGGGCTAACTGGGCAATGGTTGCTGGGAGG
GCCTTGTCATTGTACAGGCTTCACAGGCAGAGAAAACCGACTGGCAGCCATGGCCAACAACTGCAAAAGGGCACTGGTGG
ACCAATGCGCCTCTATGTGGGTTCCCTGCACTTCAGTATCACTGAAGTCATGCTCTGAGGCATCTTTGAGCCCTTTGGTA
AAATCGATAATGTTGTCTGATGAAGGACTCAGATTCAGGCCGCTCTAAAGGTTAGGGTTTCATCATGTTCTCTGAGTCTG
AGTGTGCCCAGCGGGCCCTGGAACAGTTGAATGGCTTTGAGCTTGCTGGTCCACCTATGAGGGTTGGCCACGTGACTGAG
CCACTGGATCATGGCACACACATCACTTTCCCTGATGCGGACCAGGAGCTGGATCTGGGATCAGCAGGTGGACGTTTGCA
GCTTATGGCCAAACTGGCAGAAGGCTCTGGAATCCAACTGCCAACTACCACCGCTGCTGCTGCTGCCTTGCAACTGAATG
GAGCAGTTCCCCTGGGTGCGCTGAACCCAGCAGCTCTGACTGCTCTGAGTCCAGCCCTGAACCTTACCTCCCAGTGCTTC
CAGCTCTCCAGTCTCTTTACCCCCCAGACCATG

Alignment

ORF - retro_cjac_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.08 %
• Parental protein coverage: 64.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  EPIDNLSPEERDARTVFCMQLAA-RIRPR-DLEDFFSAVG-KVRDVRIISDRN-SRRSKGIAYVE-FCEI
          EPIDNLSPEERDARTVFC.QLAA.RIRP..DLEDF.SAV..KVR.VR.ISDRN....SKGIA.VE..CEI
Retrocopy EPIDNLSPEERDARTVFCTQLAA<RIRPE<DLEDFCSAVA<KVRHVRVISDRN<LMHSKGIASVE<ICEI

Parental  QSVPLAIGLTGQRLLGVP-IIVQASQAEK-NRLAAMANN-LQKGTGGPMRLYVGSLHFNITEDMLRGIFE
          QSVPLAIGLTGQ.LLG.P..IVQASQAEK.NRLAAMANN.LQKGTGGPMRLYVGSLHF.ITE.ML.GIFE
Retrocopy QSVPLAIGLTGQWLLGGP>VIVQASQAEK<NRLAAMANN<LQKGTGGPMRLYVGSLHFSITEVML*GIFE

Parental  PFGKIDNIV-LMKDSDTGRSKGYGFITFSDSECARRAMDQLNGFELAGRPMRVGHVTEQLDGGTDITFPD
          PFGKIDN.V.LMKDSD.GRSKG.GFI.FS.SECA.RA..QLNGFELAG.PMRVGHVTE.LD.GT.ITFPD
Retrocopy PFGKIDNVV<LMKDSDSGRSKG*GFIMFSESECAQRALEQLNGFELAGPPMRVGHVTEPLDHGTHITFPD

Parental  GDQELDLGSAGGCLQLMAKLAEGSGIQLPST--QAAALQLNGAVPLGALNPAVLTALSPALNLASQCFQL
          .DQELDLGSAGG.LQLMAKLAEGSGIQLP.T...AAALQLNGAVPLGALNPA.LTALSPALNL.SQCFQL
Retrocopy ADQELDLGSAGGRLQLMAKLAEGSGIQLPTTTAAAAALQLNGAVPLGALNPAALTALSPALNLTSQCFQL

Parental  SSLFTPQTM
          SSLFTPQTM
Retrocopy SSLFTPQTM

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	20.59 RPM
SRP051959_heart	0.00 RPM	18.33 RPM
SRP051959_kidney	0.02 RPM	25.09 RPM
SRP051959_liver	0.00 RPM	15.40 RPM
SRP051959_lung	0.00 RPM	24.16 RPM
SRP051959_lymph_node	0.00 RPM	25.59 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.07 RPM
SRP051959_spleen	0.00 RPM	24.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1069 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1069 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008482	1 retrocopy	retro_cjac_1069 ,
Callithrix jacchus	ENSCJAG00000017535	1 retrocopy	retro_cjac_2199,
Myotis lucifugus	ENSMLUG00000012923	1 retrocopy	retro_mluc_2430,
Ochotona princeps	ENSOPRG00000001092	2 retrocopies	retro_opri_126, retro_opri_412,
Pan troglodytes	ENSPTRG00000006151	1 retrocopy	retro_ptro_3108,
Ictidomys tridecemlineatus	ENSSTOG00000010354	1 retrocopy	retro_itri_1902,