RetrogeneDB ID: retro_ptro_1872

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:33115107..33115406(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE4
• Ensembl ID: ENSPTRG00000012105
• Aliases: None
• Description: polymerase (DNA-directed), epsilon 4, accessory subunit [Source:HGNC Symbol;Acc:18755]

Sequence

>retro_ptro_1872
GAGGGGCAACCTGGTGGGGAGGCATAGGTCCCACAGCCCCAAGCCCCGACGAGAGTGCCTGGGGTTCGTCCCTCGAGGCT
GCCTCGGGCCCAGCGAAGGCCTTGGCGAAGGTTGACCCCAACGAGACACGGGCGGGACAGAGAACAGTCATTCTGGCCTG
AGCCGGGGAACTGTGTGTGGAGACCATTGCAAAAGATGCCTACTGCTGTGCTCAACAGGGAAACAGGAAAACCCTCCAGA
GGAGAGATTTGGATAATGCAACAGAAGCTGTGGATGAATCTGCTTTTTTGGAAGGTACT

Alignment

ORF - retro_ptro_1872 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 87.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEGPAGEAAVSQPQAPTSVPGARLSRLPLAR-VKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAY
          E..P.GEA.V.QPQAPT.VPG.R.SRLP.A...KAL.K.DP..T.AGQ....ILA.A.EL.VETIAKDAY
Retrocopy EGQPGGEA*VPQPQAPTRVPGVRPSRLPRAQ<AKALAKVDPNETRAGQRTV-ILA*AGELCVETIAKDAY

Parental  CCAQQGKRKTLQRRDLDNAIEAVDEFAFLEGT
          CCAQQG.RKTLQRRDLDNA.EAVDE.AFLEGT
Retrocopy CCAQQGNRKTLQRRDLDNATEAVDESAFLEGT

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	0.04 RPM	10.10 RPM
SRP007412_cerebellum	0.07 RPM	3.41 RPM
SRP007412_heart	0.00 RPM	6.70 RPM
SRP007412_kidney	0.10 RPM	18.41 RPM
SRP007412_liver	0.00 RPM	26.48 RPM
SRP007412_testis	0.21 RPM	6.85 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1872 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1872 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1872 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2765
Gorilla gorilla	retro_ggor_1924
Pongo abelii	retro_pabe_2246

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017073	1 retrocopy	retro_amel_394,
Callithrix jacchus	ENSCJAG00000017156	1 retrocopy	retro_cjac_1087,
Cavia porcellus	ENSCPOG00000027003	1 retrocopy	retro_cpor_1102,
Felis catus	ENSFCAG00000005983	1 retrocopy	retro_fcat_790,
Homo sapiens	ENSG00000115350	1 retrocopy	retro_hsap_2765,
Gorilla gorilla	ENSGGOG00000004491	1 retrocopy	retro_ggor_1924,
Mustela putorius furo	ENSMPUG00000008356	1 retrocopy	retro_mputfur_305,
Nomascus leucogenys	ENSNLEG00000001111	1 retrocopy	retro_nleu_670,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872 ,