RetrogeneDB ID: retro_cjac_700

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:74778776..74779869(+)
• Located in intron of: ENSCJAG00000006256

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLD2
• Ensembl ID: ENSCJAG00000007954
• Aliases: None
• Description: None

Sequence

>retro_cjac_700
TCCATCCTGCGGGAGATCAGCGAGGAGCACAACCTGCTACCCCAGCCTCCTTGGAGCAAATACATCCACCCAGATGACAA
GCTGGTTTTGGAAGATGAACTGCAGTATATCAAACTAAAAGGCACTATTGATGTGTCAAAGTTGGTTATAGGGGCTGTCC
TGGCTGTGTTTGGCTGCGTGAGAGACGACAGGAAGTTTCTGGTTGAGGACCATTGCTTTGCTGACCTCGCTCCCCAGAAG
CCCACAACCCCTCTTGACACAGATAGGTTTGTGCTGCTGGTGTCCGGCCTGGGCTTGGGTGGAGGTGGAGGTGAGAGACT
GCTGGGCACCCAGCTGCTGGTGGACGTGGTGACGGGGCAGTCTGGGGATGAAGGGGAGCAGTGCAGTGCTGCCCACGTCT
CCCGGGTCATCCTTGCTGGCAACCTTCTCAGCCACAGCACCCAGAGCAGAGATTCCATCAACAAGGCCAAGTACCTCACC
AAGAAAACCCAGGCAGCCAGCGTGGAAGCTGTGAAGATGCTGGATGAGATCCTCCTGCAGCTAAGCGCCTCAATGCCCGT
GGATGTGATGCCTCGGCGAGTCTGATCCCACGAACTACACGCTCCCGCAGCAGCCCCTCCACCCCTGCATGTTCCCGCTG
GCCATTGCCTACTCCACACTCCAGCTGGTCACCAACCCCTACCAGGCCACCATTGACGGGGTCAGATTCCTGGTGACTTT
GGGACAGAATGTGAGTGACATTTTCTGATACAGCAGCATGGAGGATCACTTAGAGATCCTGGAGTAGACCCTCCGGGTCC
GTCACATCAGCCCCACAGCCCCTGACACGCTAGGTTGTTACCCATTCTACAAAACCGACCCATTCATCTTCGCAGAGTGA
CCACAGGTCTACTTTTGTGGCAGCACCCCCAGCTTTGGCTCCAAAATCATCCGAGGTCCTGAGGACCAGAGAGTGCTGTT
GGTGACCGTCCCTGACTTCAGTGCCACGCAGACCGCCTGCCTCGTGAACCTGTGCAGCCTGGCCTGCCAGCCCATCAGCT
TCTCAGGCTTCGGGGCAAAGGATGGTGACCTGGGAGGCCTGGGGCTGAGCCCC

Alignment

ORF - retro_cjac_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 77.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SILREISEEHNLLPQPSRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVED
          SILREISEEHNLLPQP..SKYIHPDD.LVLEDELQ.IKLKGTIDVSKLV.G.VLAVFG.VRDD.KFLVED
Retrocopy SILREISEEHNLLPQPPWSKYIHPDDKLVLEDELQYIKLKGTIDVSKLVIGAVLAVFGCVRDDRKFLVED

Parental  HCFADLAPQKPAPPLDIDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAG
          HCFADLAPQKP..PLD.DRFVLLVSGLGLGGGGGE.LLGTQLLVDVVTGQ.GDEGEQCSAAHVSRVILAG
Retrocopy HCFADLAPQKPTTPLDTDRFVLLVSGLGLGGGGGERLLGTQLLVDVVTGQSGDEGEQCSAAHVSRVILAG

Parental  NLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMP-GEFDPTNYTLPQQPLHPC
          NLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSAS.PVDVMP.GE.DPTNYTLPQQPLHPC
Retrocopy NLLSHSTQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASMPVDVMP>GESDPTNYTLPQQPLHPC

Parental  MFPLATAYSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGC
          MFPLA.AYSTLQLVTNPYQATIDGVRFL.T.GQNVSDIF.YSSMEDHLEILE.TLRVRHISPTAPDTLGC
Retrocopy MFPLAIAYSTLQLVTNPYQATIDGVRFLVTLGQNVSDIF*YSSMEDHLEILE*TLRVRHISPTAPDTLGC

Parental  YPFYKTDPFIFAECPHVYFCGSTPSFGSKVIRGPEDQKVLLVTVPDFSATQTACLVNLRSLACQPISFSG
          YPFYKTDPFIFAE.P.VYFCGSTPSFGSK.IRGPEDQ.VLLVTVPDFSATQTACLVNL.SLACQPISFSG
Retrocopy YPFYKTDPFIFAE*PQVYFCGSTPSFGSKIIRGPEDQRVLLVTVPDFSATQTACLVNLCSLACQPISFSG

Parental  FGAEDDDLGGLGLGP
          FGA.D.DLGGLGL.P
Retrocopy FGAKDGDLGGLGLSP

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	0.89 RPM	16.62 RPM
SRP051959_heart	0.67 RPM	28.98 RPM
SRP051959_kidney	0.87 RPM	22.79 RPM
SRP051959_liver	0.30 RPM	12.39 RPM
SRP051959_lung	0.86 RPM	15.50 RPM
SRP051959_lymph_node	0.87 RPM	16.39 RPM
SRP051959_skeletal_muscle	0.61 RPM	31.01 RPM
SRP051959_spleen	0.67 RPM	14.60 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_700 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_700 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_700 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
Canis familiaris	ENSCAFG00000002933	1 retrocopy	retro_cfam_1870,
Callithrix jacchus	ENSCJAG00000007954	1 retrocopy	retro_cjac_700 ,
Erinaceus europaeus	ENSEEUG00000006258	1 retrocopy	retro_eeur_303,
Homo sapiens	ENSG00000106628	1 retrocopy	retro_hsap_3217,
Gorilla gorilla	ENSGGOG00000004424	2 retrocopies	retro_ggor_2183, retro_ggor_2184,
Pongo abelii	ENSPPYG00000017597	1 retrocopy	retro_pabe_2665,
Pan troglodytes	ENSPTRG00000019138	1 retrocopy	retro_ptro_2236,