RetrogeneDB ID: retro_pabe_2665

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:93840899..93842010(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLD2
• Ensembl ID: ENSPPYG00000017597
• Aliases: None
• Description: polymerase (DNA directed), delta 2, accessory subunit [Source:HGNC Symbol;Acc:9176]

Sequence

>retro_pabe_2665
GGAGAACAGAGCTTTAGCCCGCAGAACGCCCATATGTATGCCACCCGCCTCATCCAAATGAGATCCTACCTGGAGAACCG
GGCCCAGCAGTACTGGGGCAGTGGAGTGGTAGTGAAGAAGCTGTGTGAGCTGCAGCCCGGGGAGAAGTGCTGTCTGGTGG
GCACTTTGTTCAAGTCCATGCCGCTGCAGCCCTCCATCCTGCAGGAGATCAATGAGGAGCACAACCTGCTCCCCCAGCCT
CCTCAGAGCAAAGACATCCACCCAGATGACGTGCTGGTCTTGGAAGATGAACTGCAGCATATCAAACTAAAAGGCACCAT
TGACGTGTCAAAGTTGGTTACAGGGACCATCCTGGCCGTGTTTGGCTCCGTGAGGGACGACGGGAAGTTTCTGGTGGAAG
ACCACTGCTTTGCTGAACTCGCTCCCCAGAAGCCCGCACCCCTGCTTGACACAGATAGGTTCCTGCTGCTGGTGTCTGGC
CTGGGCCTGGGTGGAGGTGGAGGCGAGAGCCTGTTGGGCACCCAGCTGCTAGTGGACGTGGTGACGGCGCAGCTTAGGGA
CGAAGGAGAGCAGTACAGCGCCGGCCATGTCTCCCGAGTCATCCTTGAAGGCAGCCTCCTCAGCCACAGCACCCAGAGCA
GAGATTCTATCAATAAGGCCAAGTACCTCACCAAGAAAACCCAGGCAGCCAGTGTGGAGGCCATGAAGATGCTGGATGAG
ATCCTCCTGCAGCTGAGCTCCTCAGTGCCCGTGGACGTGATGCCAGGTGAGTTTGATCCCACCAACTACACACTCCCCCA
GCAGCCCCTCCACCCCTGCATGTTCCTGCTGGCCACTGCCTAACTCCATGCTCCAGCTAGTCATCAAACCTTACAAGGCC
ACCATTGATGGAGTCAGATTCCTGGGGACATCAGGACAGAATATGAGTGACATTTTCCGATACAGCAGCATGGAGGATCA
CTTGGAGATCCTGGAGTGGACCCTGCCGGTCCGTCACATCAGTCCCACAACCCCTGACACCCTAGGTTGTTACCCCTTCT
GCAAAACCGACCCGTTCTTCTTCCCAGAGTGCCCGCATGTCTACTTTTGTGGCAGCACCCCCAGCTTTGGC

Alignment

ORF - retro_pabe_2665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 73.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GERSFNRQYAHIYATRLIQMRPFLENRAQQHWGSGVGVKKLCELQPEEKCCVVGTLFKAMPLQPSILREI
          GE.SF..Q.AH.YATRLIQMR..LENRAQQ.WGSGV.VKKLCELQP.EKCC.VGTLFK.MPLQPSIL.EI
Retrocopy GEQSFSPQNAHMYATRLIQMRSYLENRAQQYWGSGVVVKKLCELQPGEKCCLVGTLFKSMPLQPSILQEI

Parental  SEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADL
          .EEHNLLPQPP.SK.IHPDD.LVLEDELQ.IKLKGTIDVSKLVTGT.LAVFGSVRDDGKFLVED.CFA.L
Retrocopy NEEHNLLPQPPQSKDIHPDDVLVLEDELQHIKLKGTIDVSKLVTGTILAVFGSVRDDGKFLVEDHCFAEL

Parental  APQKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSHS
          APQKPAP.LDTDRF.LLVSGLGLGGGGGESLLGTQLLVDVVT.QL.DEGEQ.SA.HVSRVIL.G.LLSHS
Retrocopy APQKPAPLLDTDRFLLLVSGLGLGGGGGESLLGTQLLVDVVTAQLRDEGEQYSAGHVSRVILEGSLLSHS

Parental  TQSRDSINKAKYLTKKTQAASVEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLATA
          TQSRDSINKAKYLTKKTQAASVEA.KMLDEILLQLS.SVPVDVMPGEFDPTNYTLPQQPLHPCMF.LATA
Retrocopy TQSRDSINKAKYLTKKTQAASVEAMKMLDEILLQLSSSVPVDVMPGEFDPTNYTLPQQPLHPCMFLLATA

Parental  -YSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYKT
          ..S.LQLV..PY.ATIDGVRFLGTSGQN.SDIFRYSSMEDHLEILEWTL.VRHISPT.PDTLGCYPF.KT
Retrocopy >NSMLQLVIKPYKATIDGVRFLGTSGQNMSDIFRYSSMEDHLEILEWTLPVRHISPTTPDTLGCYPFCKT

Parental  DPFIFPECPHVYFCGNTPSFG
          DPF.FPECPHVYFCG.TPSFG
Retrocopy DPFFFPECPHVYFCGSTPSFG

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	43.57 RPM
SRP007412_cerebellum	0.00 RPM	29.31 RPM
SRP007412_heart	0.00 RPM	36.97 RPM
SRP007412_kidney	0.00 RPM	60.39 RPM
SRP007412_liver	0.00 RPM	26.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2665 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2665 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3217
Pan troglodytes	retro_ptro_2236
Gorilla gorilla	retro_ggor_2184

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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,