RetrogeneDB ID: retro_cjac_803

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:89941371..89941947(-)
• Located in intron of: ENSCJAG00000019689

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSCJAG00000001470
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_cjac_803
ATGTCGAAGGTCAGCCTGGCCACCCGGGCCCTCAGGAAGCCCGAGGTCGGCAGTGTGATCTGGACCATCATTCGGGCAGG
CCAGGCCATGCCCGGGCCCCCACTAGGTCCAGTGTTGGGTCAGCAAGGTGTTTCCATCAACCGGTTTTGCAAGGAGTTCA
ATGAGAGGACAAAGGACATCAAGGAAGGCATTCCTCTGCCTACCAAGATTTTTGTGAAGCCTGACAGAACATTTGACATG
AAGATTGGACAGCCCACTATTTCCTACTTCCTGAAGGCAGCAGCTGGGATTGAGAAGGGGGCCCAGCAGACAGGGAAAGA
GGTGGCAGGCCTGGTGACCTTGAAGCATGTGTATGAGATTGCCCTTGTCAAAGCTCAGGATTAGGTATTCGTCCTGCAGG
ACGTACCCCTGTCCTCTGTTGTCCGCTCCATCATTGGGTCTGCCCATTCCATGGGCATTCGTGTGGTGAAGGACCTGGGT
TCAGAAGAGCTTGCAGCTTTCCTGAAGGAACGAGCCATCTTCCTGGCTGCTCAGAAGGAGGCAGATTTGGCTGCCCAGGA
AGAAGCTGCCAAGAAG

Alignment

ORF - retro_cjac_803 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.71 %
• Parental protein coverage: 98.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSRVSRATRALRKPEVGGVIRTIVRAGQAMPGPPLGPVLGQRGVSINQFCKEFNERTKDIKKGIPLPTKI
          .S.VS.ATRALRKPEVG.VI.TI.RAGQAMPGPPLGPVLGQ.GVSIN.FCKEFNERTKDIK.GIPLPTKI
Retrocopy MSKVSLATRALRKPEVGSVIWTIIRAGQAMPGPPLGPVLGQQGVSINRFCKEFNERTKDIKEGIPLPTKI

Parental  FVKPDRTFDIKIGQPTISYFLKAAAGIEKGARQTGKEVAGLVTLKHVYEIALVKAQDEVFVLQDVPLSSV
          FVKPDRTFD.KIGQPTISYFLKAAAGIEKGA.QTGKEVAGLVTLKHVYEIALVKAQD.VFVLQDVPLSSV
Retrocopy FVKPDRTFDMKIGQPTISYFLKAAAGIEKGAQQTGKEVAGLVTLKHVYEIALVKAQD*VFVLQDVPLSSV

Parental  VRSIIGSARSMGIRVVKDLGSEELAAFQKERAIFLAAQKEADLAAQEEAAKK
          VRSIIGSA.SMGIRVVKDLGSEELAAF.KERAIFLAAQKEADLAAQEEAAKK
Retrocopy VRSIIGSAHSMGIRVVKDLGSEELAAFLKERAIFLAAQKEADLAAQEEAAKK

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	0.40 RPM	14.02 RPM
SRP051959_heart	0.12 RPM	13.73 RPM
SRP051959_kidney	0.27 RPM	13.13 RPM
SRP051959_liver	0.24 RPM	18.95 RPM
SRP051959_lung	0.47 RPM	9.01 RPM
SRP051959_lymph_node	0.78 RPM	10.87 RPM
SRP051959_skeletal_muscle	0.24 RPM	24.28 RPM
SRP051959_spleen	0.44 RPM	9.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_803 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_803 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_803 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803 ,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,