RetrogeneDB ID: retro_pabe_2246

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:114370918..114371185(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLE4
• Ensembl ID: ENSPPYG00000012258
• Aliases: None
• Description: polymerase (DNA-directed), epsilon 4, accessory subunit [Source:HGNC Symbol;Acc:18755]

Sequence

>retro_pabe_2246
CAGCCCCAAGCCCCGACGAGAGTGCCTGGGGCTCATCCCTCGAGGCTGCCTTGGGCACCAGCGAAGGCCTTGGCGAAGGC
TGACCGCAAGGAGACAGGGGCGGGACAGAGAACAGTCATTCTGGCCTGAGCCAGGGAACTGTGTGTGGAGACCATTGCAA
AAGATGCCTACTGCTGTGCTCAACAGGGAAACAGGAAAACCCTCCAGAGGAGAGATTTGGATAATTCAATAGAAGCTGTG
GATGAATCTGCTTTTTTGGAAGGTACT

Alignment

ORF - retro_pabe_2246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.56 %
• Parental protein coverage: 76.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPQAPTSAPGARLSRLPLARVKALVKADPDVTLAGQEAIFILARAAELFVETIAKDAYCCAQQGKRKTLQ
          QPQAPT..PGA..SRLP.A..KAL.KAD...T.AGQ....ILA.A.EL.VETIAKDAYCCAQQG.RKTLQ
Retrocopy QPQAPTRVPGAHPSRLPWAPAKALAKADRKETGAGQRTV-ILA*ARELCVETIAKDAYCCAQQGNRKTLQ

Parental  RRDLDNAIEAVDEFAFLEGT
          RRDLDN.IEAVDE.AFLEGT
Retrocopy RRDLDNSIEAVDESAFLEGT

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	0.06 RPM	26.82 RPM
SRP007412_cerebellum	0.00 RPM	10.34 RPM
SRP007412_heart	0.00 RPM	11.71 RPM
SRP007412_kidney	0.00 RPM	110.78 RPM
SRP007412_liver	0.00 RPM	34.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2246 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2246 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2765
Pan troglodytes	retro_ptro_1872
Gorilla gorilla	retro_ggor_1924

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 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	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246 ,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,