RetrogeneDB ID: retro_cjac_3969

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286451.1:316808..317192(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PQLC3
• Ensembl ID: ENSCJAG00000006801
• Aliases: None
• Description: PQ loop repeat containing 3 [Source:HGNC Symbol;Acc:28503]

Sequence

>retro_cjac_3969
CTCTCCAGGTTCCTGGTGTTTCTCCGGTACCAGTGTTACTATGGCTATCCGCCACTGACCTACCTGGAGTAGTACCCCAT
CCTCATCGCACAAGATGTCATCCTCCTGCTCTGTATCTTTCATTTTAACGGGAAAGTGAAGCAGGCCACGCCCTATGTCG
CTGTATTGGCGTCTTCTTGGTTCGTCCTCGCCCTGCAGAAGTGGATCATAGACCTGGCCATGAATTTCTGTACTTTCATC
AGTGCGGCCAGTAAGTTTACGCAGCTCCAGTGTCTGTGGAAGACGAGAGACTCGGGAGCGGTGAGTGCGCTGACTTGGAG
CCTCTCCTCCTACACCTGTGCAACAAGAATAATCACAACTTTAATGACCACCGATGATTTTACA

Alignment

ORF - retro_cjac_3969 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 75.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAGFLVFLRYQCYYGYPPLTYLE-YPILIAQDVILLFCIFHFNGNVKQAMPYHLVRLASSWFVLALQKWI
          L..FLVFLRYQCYYGYPPLTYLE.YPILIAQDVILL.CIFHFNG.VKQA.PY..V.LASSWFVLALQKWI
Retrocopy LSRFLVFLRYQCYYGYPPLTYLE*YPILIAQDVILLLCIFHFNGKVKQATPYVAV-LASSWFVLALQKWI

Parental  IDLAMNFCTFISAASKFTQLQCLWKTRDSGAVSALTWSLSAYTCATRIITTFMTTNDFT
          IDLAMNFCTFISAASKFTQLQCLWKTRDSGAVSALTWSLS.YTCATRIITT.MTT.DFT
Retrocopy IDLAMNFCTFISAASKFTQLQCLWKTRDSGAVSALTWSLSSYTCATRIITTLMTTDDFT

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	3.86 RPM
SRP051959_heart	0.00 RPM	4.16 RPM
SRP051959_kidney	0.02 RPM	3.44 RPM
SRP051959_liver	0.00 RPM	3.44 RPM
SRP051959_lung	0.00 RPM	5.03 RPM
SRP051959_lymph_node	0.00 RPM	4.57 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.77 RPM
SRP051959_spleen	0.00 RPM	4.22 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3969 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3969 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3969 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006017	3 retrocopies	retro_chof_1902, retro_chof_2195, retro_chof_717,
Callithrix jacchus	ENSCJAG00000006801	1 retrocopy	retro_cjac_3969 ,
Dasypus novemcinctus	ENSDNOG00000015960	1 retrocopy	retro_dnov_2157,
Macropus eugenii	ENSMEUG00000009376	1 retrocopy	retro_meug_1167,
Mus musculus	ENSMUSG00000045679	2 retrocopies	retro_mmus_1352, retro_mmus_2875,