RetrogeneDB ID: retro_pabe_283

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:106578159..106578893(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSPPYG00000019499
• Aliases: None
• Description: prostaglandin reductase 1 [Source:HGNC Symbol;Acc:18429]

Sequence

>retro_pabe_283
ATGATTCATGCTAAGAGATGGACCCTGAAGAAGCACTTTGTTGGCAATCCTACTAATAGTGACTTTGAGTTGAAGACAGC
TGAGCTCCCACCCTTAAAAAATAGAGAGGTCCTGCTTGAAGCTTTGTTCCTCACTGGGGACCCTTACATGAGAGTGGCAG
CCAAAAGACTGAAGGAAGGTGATACAATGATGGGGCAGCAAGTGGCCAGATCTGTGGAAAGTAAAAACACAGCCTTACCA
ACAGGAACTATTGTACTGGCTCCTTCAGGCTGGACGGCACACTCTATTGCTGATAGAAAAAATCTGGAAAAGCTGCCAAC
AGAATGGCCTGACACAGTACCACTGTCTCTGGCTCTGGGGACAGTTAGCATGACAGGCCTCACTGCCTACTTTGGCCTAC
TTGACATCTGTGGTGTGAAGGGTGGAGAAACAGTGATGGTTAATGCAGCAGCTGGAGCTGTGGGCTCTGTTTTGGGGCAG
ATTACAAAGCTCAAGGGCTGCAAAGTGGTTGGAGCAGTAGGATCTGACAAGAAGACTGCCTACCTTAAAAAGCTTGGATC
TGATGTCTTTAACTACAAGACAGTAGAGTCTTTGAAGAAACTTTGAAGAAAGCCTCTCGTGATGGTTACAATTGTTATTT
TGATAATGTAAGTGGATGGTTTTCAAACACTGTTATCTCCCAGATGAAGAAATTTGGAAGAATTGCCATATGTGGAGCTA
TCTCCATACATAAC

Alignment

ORF - retro_pabe_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.59 %
• Parental protein coverage: 74.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVRTKTWTLKKHFVGYPTNSDFELKTAELPPLKNGEVLLEALFLTVDPYMRFAARSLKEGDKMMGQQVAR
          M...K.WTLKKHFVG.PTNSDFELKTAELPPLKN.EVLLEALFLT.DPYMR.AA..LKEGD.MMGQQVAR
Retrocopy MIHAKRWTLKKHFVGNPTNSDFELKTAELPPLKNREVLLEALFLTGDPYMRVAAKRLKEGDTMMGQQVAR

Parental  VVESKNAALPKGTIVLASPGWTTHSISDGKDLEKLLTEWPDTIPLSLALGTVGMPGLTAYFGLLEICGVK
          .VESKN.ALP.GTIVLA..GWT.HSI.D.K.LEKL.TEWPDT.PLSLALGTV.M.GLTAYFGLL.ICGVK
Retrocopy SVESKNTALPTGTIVLAPSGWTAHSIADRKNLEKLPTEWPDTVPLSLALGTVSMTGLTAYFGLLDICGVK

Parental  GGETVMVNAAAGAVGSVVGQIAKLKGCKVVGAAGSDEKVAYLQKLGFDVVFNYKTVESL-EETLRKASPD
          GGETVMVNAAAGAVGSV.GQI.KLKGCKVVGA.GSD.K.AYL.KLG.D.VFNYKTVESL.EETL.KAS.D
Retrocopy GGETVMVNAAAGAVGSVLGQITKLKGCKVVGAVGSDKKTAYLKKLGSD-VFNYKTVESL<EETLKKASRD

Parental  GYDCYFDNVGGEFSNTVIGQMKKYGRIAICGAISTYN
          GY.CYFDNV.G.FSNTVI.QMKK.GRIAICGAIS..N
Retrocopy GYNCYFDNVSGWFSNTVISQMKKFGRIAICGAISIHN

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	1.44 RPM
SRP007412_cerebellum	0.00 RPM	0.61 RPM
SRP007412_heart	0.00 RPM	3.52 RPM
SRP007412_kidney	0.00 RPM	745.37 RPM
SRP007412_liver	0.00 RPM	506.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_283 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_283 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290, retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283 ,