RetrogeneDB ID: retro_cjac_736

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:114138646..114139069(+)
• Located in intron of: ENSCJAG00000017438

Retrocopy information

• Ensembl ID: ENSCJAG00000021920
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSCJAG00000007312
• Aliases: None
• Description: None

Sequence

>retro_cjac_736
AGTGAGTCTTTGGTGGTTTGTGATGTTGCTGAAGATTTAGCGGAAAAGCTGAGAAAGTTTCGTTTTTGCAAAGAAACGAA
CAATGCTGCTATTATAATGAAGATTGACAAGGATAAGTGCCTGGTGGTACTGGATGAGGAACTTGAGGGCATTTCACCAG
ATGAACTTAAAGACGAACTACCTGAACGACAACCTCGCTTCACTGTGTATAGTTATAAATATCAACATGACAATGGAAGA
GTTTCATATCCTCTGTGCTTTATTTTCTCCAGTCCTGTTGGTTGTAAGCCTGAACAACAGATGATGTATGCTGGGAGTAA
GAATAAGCTAGTCCAGACAGCTGACCTAACCAAGGTATTTGAAATAAGAAATACCGAAGACCTAACTGAAGAATGGTTAT
GTGAGAAACTTGGATTTTTACAC

Alignment

ORF - retro_cjac_736 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.22 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SESLVVCDVAEDLVEKLRKFRFRKETNNAAIISKLKKNGRLVYLWETCSSVAPWVLSSNFSFFNLRKTFI
          SESLVVCDVAEDL.EKLRKFRF.KETNNAAII.K..K...LV.L.E......P..L.........R.T..
Retrocopy SESLVVCDVAEDLAEKLRKFRFCKETNNAAIIMKIDKDKCLVVLDEELEGISPDELKDELPERQPRFT--

Parental  VYSYKYQHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLREKLG
          VYSYKYQHD.GRVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTA.LTKVFEIRNTEDLTEEWL.EKLG
Retrocopy VYSYKYQHDNGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTADLTKVFEIRNTEDLTEEWLCEKLG

Parental  FFH
          F.H
Retrocopy FLH

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	0.91 RPM	4.17 RPM
SRP051959_heart	0.70 RPM	3.39 RPM
SRP051959_kidney	1.13 RPM	3.90 RPM
SRP051959_liver	0.74 RPM	2.56 RPM
SRP051959_lung	1.20 RPM	3.84 RPM
SRP051959_lymph_node	0.64 RPM	3.93 RPM
SRP051959_skeletal_muscle	0.20 RPM	1.92 RPM
SRP051959_spleen	1.18 RPM	4.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_736 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_736 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007312	1 retrocopy	retro_cjac_736 ,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,