RetrogeneDB ID: retro_ptro_2236

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:22108098..22109208(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLD2
• Ensembl ID: ENSPTRG00000019138
• Aliases: None
• Description: Pan troglodytes polymerase (DNA directed), delta 2, accessory subunit (POLD2), mRNA. [Source:RefSeq mRNA;Acc:NM_001246468]

Sequence

>retro_ptro_2236
GGAGAACAGAGCTTTAGCCCGCAGAACGCCCATATGTATGCCACCCGCCTCATCCAAATGAGATCCTACCTGGAGAACCG
GGCCCAGCAGCACTGGGGCAGTGGAGCGGTAGTGAAGAAGCTGCGCGAGCTGCAGCCCGGGGAGAAGCGCTGTGTGGTGG
GCACTTTGTTCAAGTCCATGCTGCTGCAGCCCTCCATCCTGCAGGAGATCAGTGAGGAGCACAACCTGCTCCCGCAGCCT
CCTCGGAGCAAATACATCCACCCAGATGACGTGCTGGTCTTGGAAGATGAACTGCAGCGTATCAAACTAAAAGGCACCAT
TGACGTGTCAAAGTTGGTTACAGGGACCATCCTGGCCGTGTTTGGCTCCGTGAGGGACGACGGGAAGTTTCTGGTGGAAG
ACCACTGCTTTGCTGACCTCACACCAACAAGCCCGCACCCCTGCTTGACACAGATAGGTTCCTGCTACTGGTGTCTGGCC
TGGGCCTGGGTGGAGGTGGAGGCGAGAGCCTGCTGGGCACCCAGCTGCTGGTGGACGTGGTGACGGGGCAGCTTAGGGAC
GAAGGGGAGCAGTTCAGCACGGCCCACGTCTCCCGAGTTGTCCTTGAAGGCAACCTCCTCAGCCACAGCACCCAGAGCAG
AGATTCTATCGATAAGGCCAAGTACCTCACCAAGAAAACCCAGGCAGCCAGCGTGGAGGCCGTGAAGATGCTGGATGAGA
TCCTCCTGCAGCTGAGCTCCTCAGTGCCTGTGGACGTGATGCCAGGCGAGTTTGATCCCACCAACTACACACTCCCCCAG
CAGCCCCTCCACCCCTGCATGTTCCTGCTGGCCACTGCCTAACTCCACACTCCAGCTAGTCATCAAACCTTACCAGGCCA
CCATTGATGGAGTCAGATTCCTGGGGACATCAGGACAGAACATGAGTGACATTTTCCGATACAGCAGCATGGAGGATCAC
TTGGAGATCCTGGAGTGGACACTGCGGGTCCGTCACATCAGTCCCACAACCCCTGACACCCTAGGTTGTTACCCCTTCTG
CAAAACCGACCCGTTCTTCTTCCCAGAGTGCCCGCATGTCTACTTTTGTGGCAGCACCCCCAGCTTTGGC

Alignment

ORF - retro_ptro_2236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.52 %
• Parental protein coverage: 78.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GERSFSRQYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREI
          GE.SFS.Q.AH.YATRLIQMR..LENRAQQHWGSG..VKKL.ELQP.EK.CVVGTLFK.M.LQPSIL.EI
Retrocopy GEQSFSPQNAHMYATRLIQMRSYLENRAQQHWGSGAVVKKLRELQPGEKRCVVGTLFKSMLLQPSILQEI

Parental  SEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADL
          SEEHNLLPQPPRSKYIHPDD.LVLEDELQRIKLKGTIDVSKLVTGT.LAVFGSVRDDGKFLVED.CFADL
Retrocopy SEEHNLLPQPPRSKYIHPDDVLVLEDELQRIKLKGTIDVSKLVTGTILAVFGSVRDDGKFLVEDHCFADL

Parental  AP-QKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSH
          .P..KPAP.LDTDRF.LLVSGLGLGGGGGESLLGTQLLVDVVTGQL.DEGEQ.S.AHVSRV.L.GNLLSH
Retrocopy TP<NKPAPLLDTDRFLLLVSGLGLGGGGGESLLGTQLLVDVVTGQLRDEGEQFSTAHVSRVVLEGNLLSH

Parental  STQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLAT
          STQSRDSI.KAKYLTKKTQAASVEAVKMLDEILLQLS.SVPVDVMPGEFDPTNYTLPQQPLHPCMF.LAT
Retrocopy STQSRDSIDKAKYLTKKTQAASVEAVKMLDEILLQLSSSVPVDVMPGEFDPTNYTLPQQPLHPCMFLLAT

Parental  A-YSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYK
          A..STLQLV..PYQATIDGVRFLGTSGQN.SDIFRYSSMEDHLEILEWTLRVRHISPT.PDTLGCYPF.K
Retrocopy A>NSTLQLVIKPYQATIDGVRFLGTSGQNMSDIFRYSSMEDHLEILEWTLRVRHISPTTPDTLGCYPFCK

Parental  TDPFIFPECPHVYFCGNTPSFG
          TDPF.FPECPHVYFCG.TPSFG
Retrocopy TDPFFFPECPHVYFCGSTPSFG

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	43.35 RPM
SRP007412_cerebellum	0.00 RPM	53.02 RPM
SRP007412_heart	0.00 RPM	46.08 RPM
SRP007412_kidney	0.00 RPM	79.89 RPM
SRP007412_liver	0.00 RPM	116.76 RPM
SRP007412_testis	0.11 RPM	105.28 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2236 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2236 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3217
Gorilla gorilla	retro_ggor_2184
Pongo abelii	retro_pabe_2665

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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 ,