RetrogeneDB ID: retro_cjac_2736

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:75669316..75669760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN37
• Ensembl ID: ENSCJAG00000010100
• Aliases: None
• Description: lin-37 homolog (C. elegans) [Source:HGNC Symbol;Acc:33234]

Sequence

>retro_cjac_2736
ATGTTCCCCCTGAAGGCGAAAGTAGAGAAATCAGAGCTGGAGATGGCCAAAGCCCGGAACCAACTGGACGCCATCCTGCA
GTGTCTGCTGGAGAAGAGTCACATGGACAGGGAGCGTCTGGATGAGGAAGCTGGGAAAATTCCCTCAGACACCCACAATA
AGGACTGCTCCATTGCAGCCACTGGCAAAAGGCCTTCTGCCCGCTTCCCCTAGCAGCGGAGGAAGAAGAGGAGGGAAATG
GATGACGGGCTGGCTGAGGGAGGGCCGCAGCGATCAAACACATATGTGATCAAGCTGTTCGACCTGAGCGTGGACTTGGC
CCAGTTCAGTGAGAACACGCCACTCTACCTGATATGCCGTGCCTGGATGTGAAACAGCCCCTCTGTGCGCGAGCGTGAGT
GCTCTCCCAGCTCACTCCTGCCCTCGCTGCCTGAGGATGAGGAC

Alignment

ORF - retro_cjac_2736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 60.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFPVKVKVEKSELEMAKARNQLDAVLQCLLEKSHMDRERLDEEAGKTPSDTHNKDCSIASTGKR--VDWP
          MFP.K.KVEKSELEMAKARNQLDA.LQCLLEKSHMDRERLDEEAGK.PSDTHNKDCSIA.TGKR.....P
Retrocopy MFPLKAKVEKSELEMAKARNQLDAILQCLLEKSHMDRERLDEEAGKIPSDTHNKDCSIAATGKRPSARFP

Parental  ERVGKELRGYARMLTHSHPHLPDTYVIKLFDRSVDLAQFSENTPLYPICRAWMRNSPSVRERECSPSSPL
          ....K..R.....L....P....TYVIKLFD.SVDLAQFSENTPLY.ICRAWM.NSPSVRERECSPSS.L
Retrocopy *QRRKKRREMDDGLAEGGPQRSNTYVIKLFDLSVDLAQFSENTPLYLICRAWM*NSPSVRERECSPSSLL

Parental  PPLPEDEE
          P.LPEDE.
Retrocopy PSLPEDED

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	2.13 RPM
SRP051959_heart	0.42 RPM	3.19 RPM
SRP051959_kidney	0.31 RPM	2.84 RPM
SRP051959_liver	0.26 RPM	1.99 RPM
SRP051959_lung	0.37 RPM	2.81 RPM
SRP051959_lymph_node	0.43 RPM	3.90 RPM
SRP051959_skeletal_muscle	0.74 RPM	5.15 RPM
SRP051959_spleen	0.29 RPM	2.75 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2736 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010100	1 retrocopy	retro_cjac_2736 ,
Echinops telfairi	ENSETEG00000004801	1 retrocopy	retro_etel_199,
Mus musculus	ENSMUSG00000036845	1 retrocopy	retro_mmus_2542,
Tursiops truncatus	ENSTTRG00000003834	1 retrocopy	retro_ttru_1074,