RetrogeneDB ID: retro_cjac_1371

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:1274533..1274806(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM4
• Ensembl ID: ENSCJAG00000021370
• Aliases: None
• Description: LYR motif containing 4 [Source:HGNC Symbol;Acc:21365]

Sequence

>retro_cjac_1371
ATGGCAGCCTCCAGCCGCGCACAAGTGTTAGATCTGTACCGGGCTATGCTGAGAGAAAGCAAGCGTCTCAGCACCTACAA
TTACAGAACGTATGCTGTCAGGAGGATAAGAGATGCCTTCAGAGAAAATAAAAATGTAAAGGATCCTGTAGAAATTCAAA
CCCAGGTGAATAAAGCCAAGAGAGACCTTGGAATAATTCGTCGACAGGTCCACATTGGCCAACTGTATTCAACTGACAAG
CTGATTATTGAGAATCAAGACATGCCCAGGACC

Alignment

ORF - retro_cjac_1371 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASSRAQVLDLYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAKRDLGIIRRQV
          MAASSRAQVLDLYRAMLRESKR.S.YNYRTYAVRRIRDAFRENKNVKDPVEIQT.VNKAKRDLGIIRRQV
Retrocopy MAASSRAQVLDLYRAMLRESKRLSTYNYRTYAVRRIRDAFRENKNVKDPVEIQTQVNKAKRDLGIIRRQV

Parental  HIGQLYSTDKLIIENRDMPRT
          HIGQLYSTDKLIIEN.DMPRT
Retrocopy HIGQLYSTDKLIIENQDMPRT

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	1.93 RPM
SRP051959_heart	0.02 RPM	2.74 RPM
SRP051959_kidney	0.00 RPM	3.57 RPM
SRP051959_liver	0.00 RPM	4.05 RPM
SRP051959_lung	0.02 RPM	2.83 RPM
SRP051959_lymph_node	0.00 RPM	2.56 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.42 RPM
SRP051959_spleen	0.00 RPM	4.79 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1371 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1371 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
Bos taurus	ENSBTAG00000031432	1 retrocopy	retro_btau_783,
Callithrix jacchus	ENSCJAG00000021370	1 retrocopy	retro_cjac_1371 ,
Homo sapiens	ENSG00000214113	1 retrocopy	retro_hsap_194,
Macropus eugenii	ENSMEUG00000005958	1 retrocopy	retro_meug_656,
Myotis lucifugus	ENSMLUG00000028065	1 retrocopy	retro_mluc_394,
Mustela putorius furo	ENSMPUG00000000532	1 retrocopy	retro_mputfur_1459,
Mus musculus	ENSMUSG00000046573	1 retrocopy	retro_mmus_2374,
Nomascus leucogenys	ENSNLEG00000011472	1 retrocopy	retro_nleu_1002,
Rattus norvegicus	ENSRNOG00000047970	2 retrocopies	retro_rnor_1862, retro_rnor_2052,
Tursiops truncatus	ENSTTRG00000007073	1 retrocopy	retro_ttru_552,