RetrogeneDB ID: retro_cjac_2558

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:113509315..113509929(+)
• Located in intron of: ENSCJAG00000014988

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL22
• Ensembl ID: ENSCJAG00000007325
• Aliases: None
• Description: mitochondrial ribosomal protein L22 [Source:HGNC Symbol;Acc:14480]

Sequence

>retro_cjac_2558
ATGGCGGCAGCAGTACTGGATCAGTTGGGTGCGTTGTGGATACAGAACATGAGGAGCCCGGGGAAGCTGGTCTTGGGTGT
TTTACCTTAATCATATATCCACACAAGTGTTTCTCTTTACATTTCTCAAAAATAGGAGAAGGACAATAAAATTGTTTATC
CACCACAACTGCCTGGAGAACCTCAGAGACCAGCAGAAATCTACCACTGTTGAAGACAAATAAAATACAGCAAAGATAAA
ATGTGATATTTGGCAAAATTGATATGAGGAATGTCTATTGACCAGGCTTTGGCTCAGTTGGAATTCAGTGACAAAAAAGG
GGCCAAAATAATTAAAGAGGTTCTCTCAGAAGTGCAAGATATGGCAGTGAGAGACCACAATGTGGAATTCAGGTCCAATT
TATATATAGATGAGTTCACCTCAGGACAAGGCCAGTGCCTGAAACGCATCTGCTACCATGGCAGAGATTACTTTGGGATT
ATGGAGGTTTATTGCCATTATTTTGTGAAGTTGGTGGAAGGTCCCCCACCTCCACCTGAGCCACCAAAGACTGCAGTTGA
CGATGCCAAAGAGTATATTCACATCTTTGAAGCCGGACCATCGTTCGCACTCTG

Alignment

ORF - retro_cjac_2558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAVLDQLGALWIQNLRRQGKLALSVLPQSYIHTSASLDISRKWEKKNKIVYPPQLPGEPRRPAEIYHC
          MAAAVLDQLGALWIQN.R..GKL.L.VLP.SYIHTS.SL.IS.K.EK.NKIVYPPQLPGEP.RPAEIYHC
Retrocopy MAAAVLDQLGALWIQNMRSPGKLVLGVLP*SYIHTSVSLYISQK*EKDNKIVYPPQLPGEPQRPAEIYHC

Parental  RRQIKYSKDKMWYLAKLIRGMSIDQALAQLEFSDKKGAKIIKEVLLEAQDMAVRDHNVEFRSNLYIAEST
          .RQIKYSKDKM.YLAKLI.GMSIDQALAQLEFSDKKGAKIIKEVL.E.QDMAVRDHNVEFRSNLYI.E.T
Retrocopy *RQIKYSKDKM*YLAKLI*GMSIDQALAQLEFSDKKGAKIIKEVLSEVQDMAVRDHNVEFRSNLYIDEFT

Parental  SGRGQCLKRIRYHGRGYFGIMEKVYCHYFVKLVEGPPPPPEPPKTAVDHAKEYI-QHLRNRTIVHAL
          SG.GQCLKRI.YHGR.YFGIME.VYCHYFVKLVEGPPPPPEPPKTAVD.AKEYI..HL..RTIV..L
Retrocopy SGQGQCLKRICYHGRDYFGIME-VYCHYFVKLVEGPPPPPEPPKTAVDDAKEYI<SHL*SRTIVRTL

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	5.13 RPM
SRP051959_heart	0.00 RPM	6.12 RPM
SRP051959_kidney	0.00 RPM	8.43 RPM
SRP051959_liver	0.02 RPM	7.58 RPM
SRP051959_lung	0.03 RPM	6.56 RPM
SRP051959_lymph_node	0.00 RPM	5.80 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.42 RPM
SRP051959_spleen	0.02 RPM	6.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2558 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2558 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2558 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003875	1 retrocopy	retro_acar_88,
Callithrix jacchus	ENSCJAG00000007325	2 retrocopies	retro_cjac_2187, retro_cjac_2558 ,
Homo sapiens	ENSG00000082515	1 retrocopy	retro_hsap_3041,
Gorilla gorilla	ENSGGOG00000010232	1 retrocopy	retro_ggor_2095,
Mus musculus	ENSMUSG00000020514	1 retrocopy	retro_mmus_1294,
Nomascus leucogenys	ENSNLEG00000016692	1 retrocopy	retro_nleu_1928,
Pongo abelii	ENSPPYG00000015979	1 retrocopy	retro_pabe_2436,
Pan troglodytes	ENSPTRG00000017453	1 retrocopy	retro_ptro_1997,