RetrogeneDB ID: retro_cjac_696

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:66345810..66346094(+)
• Located in intron of: ENSCJAG00000016083

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSCJAG00000007700
• Aliases: None
• Description: FK506 binding protein 1B, 12.6 kDa [Source:HGNC Symbol;Acc:3712]

Sequence

>retro_cjac_696
AGAGCCAGAGCCAAGAAGAGACAAACGTGAGTGGTGTACTACAAAGGAATGCTCCAACATGGGAACAAATTTGATTTATC
CCAAGACAGAAACAAACCTTTCAAATTTAAAATTGGTGAATAGGAAGTTATCAGTGATTTTGAGGAGTACATAGTGCTAA
TGAGCTTGGGGAAGAAGGTGAACCTGACCTGCATACCTGATGTGGCATATGGAGTCCCAGGCTACTCTAGTGTCATCCCT
CCTAGTGCTACCCTGTCTTTGACATGGAACCACTCAACTTAGAG

Alignment

ORF - retro_cjac_696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.54 %
• Parental protein coverage: 87.96 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAY
          R...KK.QT.VV.Y.GMLQ.G.KFD.S.DRNKPFKF.IG..EVI..FEE....MSLG....LTC.PDVAY
Retrocopy RARAKKRQT*VVYYKGMLQHGNKFDLSQDRNKPFKFKIGE*EVISDFEEYIVLMSLGKKVNLTCIPDVAY

Parental  GATGHPGVIPPNATL-IFDVELLNLE
          G..G...VIPP.ATL..FD.E.LNLE
Retrocopy GVPGYSSVIPPSATL<VFDMEPLNLE

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	0.09 RPM
SRP051959_heart	0.04 RPM	0.70 RPM
SRP051959_kidney	0.00 RPM	0.33 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.00 RPM	1.06 RPM
SRP051959_lymph_node	0.00 RPM	0.34 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.15 RPM
SRP051959_spleen	0.00 RPM	0.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_696 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_696 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_696 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1329
Pan troglodytes	retro_ptro_906
Gorilla gorilla	retro_ggor_1036
Pongo abelii	retro_pabe_1105
Macaca mulatta	retro_mmul_2171

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696 ,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,