RetrogeneDB ID: retro_ggor_2184

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:76128821..76129931(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000024153
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POLD2
• Ensembl ID: ENSGGOG00000004424
• Aliases: None
• Description: None

Sequence

>retro_ggor_2184
GGAGAACAGAGCTTTAGCCCGCAGAACGCCCATATGTATGCCACCCGCCTCAACCAAATGAGATCCTACCTGGAGAACCG
GGCCCAGCAGCACTGGGGCAGTGGAGCGGTAGTGAAGAAGCTGCGCGAGCTGCAGCCCGGGGAGAAGTGCTGTGTGGTGG
GCACTTTGTTCAAGTCCATGCCGCTGCAGCCCTCCATCCTGCAGGAGATCAGTGAGGAGCACAACCTGCTCCCGCAGCCT
CCTCGGAGCAAATACATCCACCCAGATGACGTGCTGGTCTTGGAAGATGAACTGCAGCATATCAAACTAAAAGGCACCAT
TGACATGTCAAAGTTGGTTACAGGGACCATCCTGGCCGTGTTTGGCTCCGTGAGGGACGACGGGAAGTTTCTGGTGGAAG
ACCACTGCTTTGCTGACCTCACACCAACAAGCCCGCACCCCTGCTTGACACAGATAGGTTCCTGCTGCTGGTGTCTGGCC
TGGGCCTGGGTGGAGATGGAGGCGAGAGCCTGCTGGGCACCCAGCTGCTGGTGGACGTGGTGACGGGGCAGCTTAGGGAC
GAAGGGGAGCAGTTCAGCGCGGCCCACGTCTCCCGAGTTGTCCTTGAAGGCAACCTCCTCAGCCACAGCACCCAGAGCAG
AGATTCTATCAATAAGGCCAAGTACCTCACCAAGAAAACCCAGGCAGCCAGCGCGGAGGCCGTGAAGATGCTGGATGAGA
TCCTCCTGCAGCTGAGCTCCTCAGTGCCCGTGGACGTGATGCCAGGCGAGTTTGATCCCACCAACTACACACTCCCCCAG
CAGCCCCTCCACCCCTGCGTGTTCCTGCTGGCCACTGCCTAACTGCACGCTCCAGCTAGTCATCAAACCTTACCAGGCCA
CCATTGATGGAGTCAGATTCCTGGGGACATCAGGACAGAACATGAGTGACATTTTCCGATACAGCAGCATGGAGGATCAC
TTGGAGATCCTGGAGTGGACACTGCGGGTCCGTCACATCAGTCCCACAACCCCTGAGACCCTAGGTTGTTACCCCTTCTG
CAAAACCGACCCGTTCTTCTTCCCAGAGTGCCCGCATGTCTACTTTTGTGGCAGCACCCCCAGCTTTGGC

Alignment

ORF - retro_ggor_2184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• 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.YATRL.QMR..LENRAQQHWGSG..VKKL.ELQP.EKCCVVGTLFK.MPLQPSIL.EI
Retrocopy GEQSFSPQNAHMYATRLNQMRSYLENRAQQHWGSGAVVKKLRELQPGEKCCVVGTLFKSMPLQPSILQEI

Parental  SEEHNLLPQPPRSKYIHPDDELVLEDELQRIKLKGTIDVSKLVTGTVLAVFGSVRDDGKFLVEDYCFADL
          SEEHNLLPQPPRSKYIHPDD.LVLEDELQ.IKLKGTID.SKLVTGT.LAVFGSVRDDGKFLVED.CFADL
Retrocopy SEEHNLLPQPPRSKYIHPDDVLVLEDELQHIKLKGTIDMSKLVTGTILAVFGSVRDDGKFLVEDHCFADL

Parental  AP-QKPAPPLDTDRFVLLVSGLGLGGGGGESLLGTQLLVDVVTGQLGDEGEQCSAAHVSRVILAGNLLSH
          .P..KPAP.LDTDRF.LLVSGLGLGG.GGESLLGTQLLVDVVTGQL.DEGEQ.SAAHVSRV.L.GNLLSH
Retrocopy TP<NKPAPLLDTDRFLLLVSGLGLGGDGGESLLGTQLLVDVVTGQLRDEGEQFSAAHVSRVVLEGNLLSH

Parental  STQSRDSINKAKYLTKKTQAASAEAVKMLDEILLQLSASVPVDVMPGEFDPTNYTLPQQPLHPCMFPLAT
          STQSRDSINKAKYLTKKTQAASAEAVKMLDEILLQLS.SVPVDVMPGEFDPTNYTLPQQPLHPC.F.LAT
Retrocopy STQSRDSINKAKYLTKKTQAASAEAVKMLDEILLQLSSSVPVDVMPGEFDPTNYTLPQQPLHPCVFLLAT

Parental  A-YSTLQLVTNPYQATIDGVRFLGTSGQNVSDIFRYSSMEDHLEILEWTLRVRHISPTAPDTLGCYPFYK
          A...TLQLV..PYQATIDGVRFLGTSGQN.SDIFRYSSMEDHLEILEWTLRVRHISPT.P.TLGCYPF.K
Retrocopy A>NCTLQLVIKPYQATIDGVRFLGTSGQNMSDIFRYSSMEDHLEILEWTLRVRHISPTTPETLGCYPFCK

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	51.93 RPM
SRP007412_cerebellum	0.00 RPM	55.95 RPM
SRP007412_heart	0.00 RPM	75.58 RPM
SRP007412_kidney	0.00 RPM	62.31 RPM
SRP007412_liver	0.00 RPM	72.86 RPM
SRP007412_testis	0.00 RPM	163.58 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2184 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3217
Pan troglodytes	retro_ptro_2236
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,