RetrogeneDB ID: retro_cjac_4090

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:72259789..72260586(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDK1
• Ensembl ID: ENSCJAG00000007507
• Aliases: None
• Description: None

Sequence

>retro_cjac_4090
ATCAGGAACCAATGTAATGATATCCTTTCTACAATGGCCCAGGAAGTGATTAAATAAGGAGGCTTCAGAGTAGATTCTGT
CAGCAGACAGAGTACTCAGTACTTTTTGAATCATTTTTACATGAGTTGCCTTTCAATTAGAATGTTACTCAATCTGCACT
CTTTATTATTTCATGAAAAAGACAAAGGATGTCTATCTCTTGAAAAACATATTGCAAACATAAATACAAACTTCAAGGTA
GATGGAGTTATTAAATATGGCCATGAAAATGCTACACATCTGTGTGATCTGTATTACATGAATTATTCCAAATTCAAACT
TGAACAAGTAAATATAAAGCCCTGAGGATGACCAATATAAGTGGGTTATGTACCATCATATTTCTATCACCTGGTGTTTG
AAGTTTTCAAGAATGCAGTGAGAACAACTATGGGTCATCATATCAATGAAGTGTTTATCCCCCGATTCAAGTTCCTGTCA
CACTGGGTAATAAGGATTTGACTGTAAGATGAGTGACTGAGGAGGTAGTCTTTTTTTTGAGGAAAATGGACAGACTCTTC
ATCTGCATGTGTTCAACTGCAACACATCCTGGTGCTGAGATTTTCTGAGTGGTGCTTCCGGGTAGTTTTGGTTACAGACT
GCCTATGTCATATCTTTATGCACAATACTATCAAGGAGATCTAATGCTATATTCCCTGGTGAGTTATAAAACAGACACAG
CTTTCTATATTAAAGCACTGTCAGGAGAATCAATAGAAAGACTCCAAGTGTTTGATCAAACTGCCTGGAAATATTAC

Alignment

ORF - retro_cjac_4090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 60.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRNRHNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFGGKGKGSPSHRK
          IRN..ND...TMAQ.VI.....F.VD.V..Q..QYFL..FYMS..SIRMLLN.HSLLF..K.KG..S..K
Retrocopy IRNQCNDILSTMAQEVIK*G-GFRVDSVSRQSTQYFLNHFYMSCLSIRMLLNLHSLLFHEKDKGCLSLEK

Parental  HIGSINPNCNVVEVIKDGYENARRLCDLYYINSPELELGELNAKSPGQPIQVVYVPSHLYHMVFELFKNA
          HI..IN.N..V..VIK.G.ENA..LCDLYY.N.....L...N.K..G.PI.V.YVPS..YH.VFE.FKNA
Retrocopy HIANINTNFKVDGVIKYGHENATHLCDLYYMNYSKFKLEQVNIKP*G*PI*VGYVPSYFYHLVFEVFKNA

Parental  MRATMEHHADK-GVYPPIQVYVTLGNEDLTV-KMSDRGGGV-PLRKIDRLFNYMYSTAPRPRVETSRAVP
          .R.TM.HH.....VYPPIQV.VTLGN.DLTV.KMSD.GG....LRK.DRLF..M.STA..P..E....V.
Retrocopy VRTTMGHHINE<SVYPPIQVPVTLGNKDLTV<KMSD*GGSL>FLRKMDRLFICMCSTATHPGAEIF*VVL

Parental  LAGFGYGLPISRLYAQYFQGDLKLYSLEGYGTDAVIYIKALSTDSIERLPVYNKAAWKHY
          ...FGY.LP.S.LYAQY.QGDL.LYSL..Y.TD...YIKALS..SIERL.V....AWK.Y
Retrocopy PGSFGYRLPMSYLYAQYYQGDLMLYSLVSYKTDTAFYIKALSGESIERLQVFDQTAWKYY

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	9.23 RPM
SRP051959_heart	0.00 RPM	24.12 RPM
SRP051959_kidney	0.00 RPM	10.16 RPM
SRP051959_liver	0.00 RPM	9.18 RPM
SRP051959_lung	0.00 RPM	6.91 RPM
SRP051959_lymph_node	0.00 RPM	15.98 RPM
SRP051959_skeletal_muscle	0.00 RPM	26.71 RPM
SRP051959_spleen	0.00 RPM	9.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4090 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007507	1 retrocopy	retro_cjac_4090 ,
Cavia porcellus	ENSCPOG00000008434	1 retrocopy	retro_cpor_545,
Macaca mulatta	ENSMMUG00000022553	1 retrocopy	retro_mmul_2511,
Monodelphis domestica	ENSMODG00000009035	2 retrocopies	retro_mdom_107, retro_mdom_1447,
Otolemur garnettii	ENSOGAG00000014761	1 retrocopy	retro_ogar_509,