RetrogeneDB ID: retro_cjac_2485

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:149158376..149158636(-)
• Located in intron of: ENSCJAG00000019537

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM2
• Ensembl ID: ENSCJAG00000000905
• Aliases: None
• Description: LYR motif containing 2 [Source:HGNC Symbol;Acc:25229]

Sequence

>retro_cjac_2485
ATGGCCGCCTCCCACTTACCCTCAGCCATGCTAACATTAAAGCAGTTCATAAGAAGGCAACAAGTTCTTCTCTACAGAAG
GATTTTGCAAACAATTTGGCAAATTCCAAATGATTCTGATCGCAATTAACAGAAGGATTGGGCAAGGGAAGAATTCAGAA
GAAACAAAGTGCCACCGAAGAGGGCACAGTCCTGATGCTGATTACTCAAGGCAATATTGCAGCTCAAGGAGTTAGAAAAA
CACTTGCTTTAGCAAAATCT

Alignment

ORF - retro_cjac_2485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAATRLPPATLTLKQFIRRQQVLLLYRRILQTIRQVPNDSDRKYLKDWAREEFKRNK-SATEEDTIRMMI
          MAA..LP.A.LTLKQFIRRQQV.LLYRRILQTI.Q.PNDSDR...KDWAREEF.RNK.SATEE.T..M.I
Retrocopy MAASHLPSAMLTLKQFIRRQQV-LLYRRILQTIWQIPNDSDRN*QKDWAREEFRRNK<SATEEGTVLMLI

Parental  TQGN-MQLKELE-KTLALAKS
          TQGN..QLKELE.KTLALAKS
Retrocopy TQGN>LQLKELE<KTLALAKS

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	1.71 RPM
SRP051959_heart	0.11 RPM	1.96 RPM
SRP051959_kidney	0.02 RPM	3.57 RPM
SRP051959_liver	0.09 RPM	2.71 RPM
SRP051959_lung	0.13 RPM	1.97 RPM
SRP051959_lymph_node	0.05 RPM	1.62 RPM
SRP051959_skeletal_muscle	0.07 RPM	2.51 RPM
SRP051959_spleen	0.21 RPM	2.10 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2485 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2485 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000905	1 retrocopy	retro_cjac_2485 ,
Cavia porcellus	ENSCPOG00000015625	4 retrocopies	retro_cpor_1169, retro_cpor_1223, retro_cpor_925, retro_cpor_946,
Homo sapiens	ENSG00000083099	1 retrocopy	retro_hsap_2054,
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,