RetrogeneDB ID: retro_cjac_436

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:82133965..82134863(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSCJAG00000018746
• Aliases: None
• Description: None

Sequence

>retro_cjac_436
ATGACAGCCGAGGAGATGAAGGTGCCACAGAGTGGGGTGCAGTCGGTGACACCACCCATGGAAGGAGTGAATATCAGCCC
CAAACAGGAGGAAGGCCTGCTGAAGGTCATCAAGAGAGAAGGTGCAGGTACAGAGCTGCCCATGACTGGGGATGAAATTT
TTGTCCACTACCCTGGCTGGCGGTTAGATGGCACAAAGTTTGATTACAGTGTGGACTGCAAGGACAAATTCTCCTTTGAC
CCGGGAAAAGGGGAGGTCATCTAGGCTTGCAACATTGCCCTAGCAACTGTGAAGGTGAGGGAGGTGTGCCACATTACCTG
CAAACCAGAATATGCCTACAGTTTAGCAGGCAGGCCTCCAAAGATCCCCCCAATGCCATGCTTGTGTTTGAGGTGGAGTC
TTTTGAGTTTAAGGGAGATCTGATGGAAGAGGAAGATGGAATCATCCACAGAAAACAGACTCCCAGTGAAGGTTTTGCCA
AGCCCATTGAGGATGTTATGGGGGAGGTTGCACTGGAAAGGTACTAGAGGGACCAGCTCTTTAACCAACGGGAGCTCTGC
TTTGAGGTTGGCAAGGGGGAGAACCTGGATCTGCCTTATAATCTGGAGAGGGCCATTGAGCCCATGGGGAAAGGAGAGCA
TTCCATTGTGGACCTCAAGTCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAAAGTTCCAAATCCCACCAAATGCTGAGC
TGAAATATGAATCACACCTCAAGGGTTTTGAAAAGGCCGAGGAGTCTTGGGAGATGAATTCAAAGAGAAGCTAGAACAGA
GCACCATAGTTAAAGAACAAGGCACTGTGTACTTCAAGGAAAACAAATACAAGCAAGCTTTACTACAGTATAAGAAGATT
GTGTCATGGCTGGAATAT

Alignment

ORF - retro_cjac_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.64 %
• Parental protein coverage: 65.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTAEEMKATENGAQSAPLPVEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGWLLDGTKFDSS
          MTAEEMK....G.QS...P.EGV.ISPKQ.EG.LKVIKREG.GTE.PM.GD..FVHY.GW.LDGTKFD.S
Retrocopy MTAEEMKVPQSGVQSVTPPMEGVNISPKQEEGLLKVIKREGAGTELPMTGDEIFVHYPGWRLDGTKFDYS

Parental  LDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPPKI-PPNATLVFEVELFEFKG
          .D.KDKFSFD.GKGEVI.A..IA.AT.KV.EVCHITCKPEYAY..AG.PPKI.PPNA.LVFEVE.FEFKG
Retrocopy VDCKDKFSFDPGKGEVI*ACNIALATVKVREVCHITCKPEYAYSLAGRPPKI<PPNAMLVFEVESFEFKG

Parental  EDLTEEEDGGIIRRIRTRGEGYAKPNEGAIVEVALEGYYKDQLFDQRELRFEIGEGENLDLPYGLERAIQ
          .DL.EEED.GII.R..T..EG.AKP.E....EVALE.Y..DQLF.QREL.FE.G.GENLDLPY.LERAI.
Retrocopy -DLMEEED-GIIHRKQTPSEGFAKPIEDVMGEVALERY*RDQLFNQRELCFEVGKGENLDLPYNLERAIE

Parental  RMEKGEHSIVYLKPSYAFGKVGKEKLQIPPNAELKYELHLKSFEKAKESWEMNS-EEKLEQSTIVKERGT
          .M.KGEHSIV.LK.SYAFG.VGKEK.QIPPNAELKYE.HLK.FEKA.ESWEMNS..EKLEQSTIVKE.GT
Retrocopy PMGKGEHSIVDLKSSYAFGSVGKEKFQIPPNAELKYESHLKGFEKAEESWEMNS<KEKLEQSTIVKEQGT

Parental  VYFKEGKYKQALLQYKKIVSWLEY
          VYFKE.KYKQALLQYKKIVSWLEY
Retrocopy VYFKENKYKQALLQYKKIVSWLEY

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	12.91 RPM
SRP051959_heart	0.00 RPM	10.07 RPM
SRP051959_kidney	0.00 RPM	16.44 RPM
SRP051959_liver	0.00 RPM	24.67 RPM
SRP051959_lung	0.00 RPM	23.95 RPM
SRP051959_lymph_node	0.00 RPM	30.87 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.77 RPM
SRP051959_spleen	0.00 RPM	20.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_436 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561,
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,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,