RetrogeneDB ID: retro_cjac_548

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:74595391..74595677(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL51
• Ensembl ID: ENSCJAG00000018232
• Aliases: None
• Description: mitochondrial ribosomal protein L51 [Source:HGNC Symbol;Acc:14044]

Sequence

>retro_cjac_548
ATAGCAGGGAGCCTCTAATGCAGGGCAGGTAGGCACCTGAGGGGCTGGGTGCTTCTGGCATACAGAAGCTTCTCTCTGGG
AGTTCCTGGATTGACTCGTGTAAGGCTCCCTCCCAACCCCTCTAAGCGGTTGATGGTTGGAACAACAAGAGAGCCATGTT
TGGAGTATATGACAACACTGGGATCCTGGGAAACTGAAACGCACACCAAATAACTTGAGCAGGGACCCCAGATGACTTCA
GGCTTGGAAGGGGAATGAATTGTAACATTGTAGTCAAAAGAAAAAA

Alignment

ORF - retro_cjac_548 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.2 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGSLLCGVGRRLLDWVPLACRSFSLDVPRLMGIRLTLPPPK-VVDRWNEKRAMFGVYDNIGILGNFEKH
          .AGSL.C..GR.L..WV.LA.RSFSL.VP.L...RL...P.K..VD.WN.KRAMFGVYDN.GILGN...H
Retrocopy IAGSL*CRAGRHLRGWVLLAYRSFSLGVPGLTRVRLPPNPSK<AVDGWNNKRAMFGVYDNTGILGN*NAH

Parental  -PKELIRGPVWLRGWKGNELQRCIRKKK
          .P..L.R.P..L..WKGNEL..C..KKK
Retrocopy <PNNLSRDPR*LQAWKGNEL*HCSQKKK

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	0.13 RPM	12.91 RPM
SRP051959_heart	0.00 RPM	23.80 RPM
SRP051959_kidney	0.00 RPM	31.90 RPM
SRP051959_liver	0.00 RPM	33.86 RPM
SRP051959_lung	0.02 RPM	16.19 RPM
SRP051959_lymph_node	0.00 RPM	12.53 RPM
SRP051959_skeletal_muscle	0.00 RPM	42.10 RPM
SRP051959_spleen	0.00 RPM	14.64 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_548 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_548 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_548 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548 ,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157, retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967, retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,