RetrogeneDB ID: retro_cjac_3318

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:78520657..78521128(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSCJAG00000005116
• Aliases: None
• Description: mitochondrial ribosomal protein L2 [Source:HGNC Symbol;Acc:14056]

Sequence

>retro_cjac_3318
GAGAAGACCAAGTCAGGACCCTTTGAGGGGAAGGTTATCCAAGTCTGCTACGATCCCTGTAGGTCAGCAGACATAGCTCT
GGTTGCTGGACGCAGCCAGAAACACTGGATTATCGCTACAGAAAACATGCAGGCTGGAGATACGATCCTGAACTCTAACC
ACATACGCTGAATCACAGTTGCTGCTTGGGAAGGGGATGCACATTCATTTGGGGCTCTGCCTGTGGGGACCCTCATCAAC
AACATGGAAAGTGAGCCAGGACTGGGTGCCCAGTACATTTGAACTGCAGGGATATGTGGTGTGCTACTGTGGAAGGTGAA
TGGCACAGCCATTATCCAGCTGCCCTCTAAGAGGCAAATACAGGTGCTGGAAACGTGCATGGCAACAGTAGGCTGAGTAT
CCAACACTGATCATAACAAACGGGTCACTGGCAGGGCAGGTCACAACCACTGGCTGAGCAAGAGGCCTTCC

Alignment

ORF - retro_cjac_3318 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.62 %
• Parental protein coverage: 51.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KETNSGPFEEKVIQVRYDPCRSADIALVAGGSRKRWIIATENMQAGDRILNSNHIGRMAVAAREGDAHPL
          ..T.SGPFE.KVIQV.YDPCRSADIALVAG.S.K.WIIATENMQAGD.ILNSNHI....VAA.EGDAH..
Retrocopy EKTKSGPFEGKVIQVCYDPCRSADIALVAGRSQKHWIIATENMQAGDTILNSNHIR*ITVAAWEGDAHSF

Parental  GALPVGTLINNVESEPGRGAQYIRAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCIATVGRVSNVDHNK
          GALPVGTLINN.ESEPG.GAQYI..AG.CGVLL.KVNGTAIIQLPSKRQ.QVLETC.ATVG.VSN.DHNK
Retrocopy GALPVGTLINNMESEPGLGAQYI*TAGICGVLLWKVNGTAIIQLPSKRQIQVLETCMATVG*VSNTDHNK

Parental  RVIGKAGRNRWLGKRPN
          RV.G.AG.N.WL.KRP.
Retrocopy RVTGRAGHNHWLSKRPS

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	2.95 RPM
SRP051959_heart	0.00 RPM	4.56 RPM
SRP051959_kidney	0.00 RPM	8.03 RPM
SRP051959_liver	0.00 RPM	8.75 RPM
SRP051959_lung	0.00 RPM	4.21 RPM
SRP051959_lymph_node	0.00 RPM	3.93 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.60 RPM
SRP051959_spleen	0.00 RPM	4.24 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3318 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3318 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3318 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318 ,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,