RetrogeneDB ID: retro_cjac_1019

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:27173667..27174447(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMBS
• Ensembl ID: ENSCJAG00000013900
• Aliases: None
• Description: None

Sequence

>retro_cjac_1019
ATGTCTGGTAACGGCAACGCGACTGCAGCAGCGGAAGAAAACAGCCCAAAGATGAGAGTGATTCGTGTGGTTACCCGCAA
GAGCCAGCTTGCTCGCATACAGACGGACAGTGTGGTGGCAACACTGAAAGCCTTGTACCCTGGCCTGCAGTTTGAAATCA
TTGCTATGTCCACCACAGGGGACAAGATCCTTGATACTGCACTCTCTAAGATTGGAGAGAAGAGCTTGTTTACCAAGGAG
CTTGAACATGCCCTGGAGAGGAATGAAGTGGACCTGGTTGTTCACTCCCTGAAGGACCTGCCCACTGTGCTTCCTCCTGG
CTTCACCATAGGAGCCATCTGCAAGCGGGAAAACCCCCATGATGCTGTTGTCTTTCACCCAAAATTTGTTGGGAAGACCC
TAGAAACTTTGCCAGAAAAGAGTGTGGTGGGAACCAGCTCCCTGCGGAGAGCGGCCCAGCTGCAGAGAAAGTTCCCACAT
CTGGAGTTCAGGAGCATTCGGGGAAACCTCAACACCCGGCTTCGGAAGCTGGACGAGCAGCAGGAGTTTAGTGCGATCAT
CCTGGCAACAGCTGGCCTGCAGCGCATGGGCTGGCACAACCGGGTGGGGCAGATCCTGCACCCTGAGGAATGCATGTATG
CTGTGGGCCAGGGGGCCTTGGGTGTGGAAGTCCGAGCCAAGGACCAGGACATCTTGGATATGGTGGGTGTGCTGCATGAT
CCTGAAACTCTGCTTCGCTGCATCGCTGAAAGGGCCTTCCTGAGGCACCTGGAAGGAGGC

Alignment

ORF - retro_cjac_1019 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.85 %
• Parental protein coverage: 72.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGNGNATATVEENSPKMRVIRVGTRKSQLARIQTDSVVATLKALYPGLQFEIIAMSTTGDKILDTALSK
          MSGNGNATA..EENSPKMRVIRV.TRKSQLARIQTDSVVATLKALYPGLQFEIIAMSTTGDKILDTALSK
Retrocopy MSGNGNATAAAEENSPKMRVIRVVTRKSQLARIQTDSVVATLKALYPGLQFEIIAMSTTGDKILDTALSK

Parental  IGEKSLFTKELEHALERNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEK
          IGEKSLFTKELEHALERNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEK
Retrocopy IGEKSLFTKELEHALERNEVDLVVHSLKDLPTVLPPGFTIGAICKRENPHDAVVFHPKFVGKTLETLPEK

Parental  SVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEE
          SVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEE
Retrocopy SVVGTSSLRRAAQLQRKFPHLEFRSIRGNLNTRLRKLDEQQEFSAIILATAGLQRMGWHNRVGQILHPEE

Parental  CMYAVGQGALGVEVRAKDQDILDMVGVLHDPETLLRCIAERAFLRHLEGG
          CMYAVGQGALGVEVRAKDQDILDMVGVLHDPETLLRCIAERAFLRHLEGG
Retrocopy CMYAVGQGALGVEVRAKDQDILDMVGVLHDPETLLRCIAERAFLRHLEGG

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	0.02 RPM	2.84 RPM
SRP051959_heart	0.21 RPM	3.86 RPM
SRP051959_kidney	0.04 RPM	2.46 RPM
SRP051959_liver	0.00 RPM	4.33 RPM
SRP051959_lung	0.07 RPM	3.01 RPM
SRP051959_lymph_node	0.00 RPM	2.53 RPM
SRP051959_skeletal_muscle	1.38 RPM	3.63 RPM
SRP051959_spleen	0.00 RPM	9.05 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1019 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1019 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013900	1 retrocopy	retro_cjac_1019 ,
Tursiops truncatus	ENSTTRG00000002806	1 retrocopy	retro_ttru_1423,