RetrogeneDB ID: retro_cjac_2757

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:118501773..118502316(+)
• Located in intron of: ENSCJAG00000005224

Retrocopy information

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

Parental gene information

• Parental gene symbol: OGFRL1
• Ensembl ID: ENSCJAG00000003635
• Aliases: None
• Description: None

Sequence

>retro_cjac_2757
GACCCGGGGCCGGGCCACTTCAGTGAGGGCCCGGAGCAGGAGCCCGAGCAGCCCCTGAAGCGAGCTGGCGGGCGGCCCAG
CGCCAGACCCGCACCGGAGAGGATGCGGAGGCGGCGGGCGCCGAGCAGGGTGATGATTCCACTGAAGCAATGGCCAAACC
AAAGAGAAGTTTTTATGCTGCGAGGGATTTGTACAAGTACCGACACCAGTACCCAAACTTCAAAGATATCCGATATCAAA
ATGACTTAAGCAATCTTCGTTTTTATAAGAATAAAATTCCATTCAAGCCAGATGGTGTTTACATTAAAGAAGTTCTAAAT
AAATGGAAAGGAGATTATGAAAAACTGGAGCACAACCGCACTTAACATTCAATGGCTTTTCCCCCTGAGAGAACAGGGCT
TGAACTTTTACCCTAAAGAACTACCTACATATGAAATTGAGGAATTCAAAAAAACAAAAGAAGCAATTAGAAGATTCCTC
CTGGCTTATAAAATGATGCTAGAATTTTTTGGAGTAAAACTGACTGATAAAATTGGAAATGTT

Alignment

ORF - retro_cjac_2757 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.3 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DPGPGGGSEGPGQEPEQPAQPPERAGGRPSASPAPD-EDAEAAGAEQGDDSTEATTAKPKRSFYAARDLY
          DPGPG..SEGP.QEPE...QP..RAGGRPSA.PAP..EDAEAAGAEQGDDSTEA..AKPKRSFYAARDLY
Retrocopy DPGPGHFSEGPEQEPE---QPLKRAGGRPSARPAPE<EDAEAAGAEQGDDSTEAM-AKPKRSFYAARDLY

Parental  KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYIEEVLNKWKGDYEKLEHNHT-YIQWLFPLREQGL
          KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYI.EVLNKWKGDYEKLEHN.T..IQWLFPLREQGL
Retrocopy KYRHQYPNFKDIRYQNDLSNLRFYKNKIPFKPDGVYIKEVLNKWKGDYEKLEHNRT>NIQWLFPLREQGL

Parental  NFYAKELTTYEIEEFKKTKEAIRRFLLAYKMMLEFFGIKLTDKIGNV
          NFY.KEL.TYEIEEFKKTKEAIRRFLLAYKMMLEFFG.KLTDKIGNV
Retrocopy NFYPKELPTYEIEEFKKTKEAIRRFLLAYKMMLEFFGVKLTDKIGNV

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	0.18 RPM	16.37 RPM
SRP051959_heart	0.25 RPM	8.56 RPM
SRP051959_kidney	0.20 RPM	15.22 RPM
SRP051959_liver	0.17 RPM	8.62 RPM
SRP051959_lung	0.28 RPM	24.56 RPM
SRP051959_lymph_node	0.21 RPM	7.65 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.48 RPM
SRP051959_spleen	0.17 RPM	20.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2757 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2757 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2757 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002600	1 retrocopy	retro_chof_1780,
Callithrix jacchus	ENSCJAG00000003635	1 retrocopy	retro_cjac_2757 ,
Myotis lucifugus	ENSMLUG00000007329	1 retrocopy	retro_mluc_870,