RetrogeneDB ID: retro_pabe_2891

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:100714524..100715149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BDH2
• Ensembl ID: ENSPPYG00000025868
• Aliases: None
• Description: 3-hydroxybutyrate dehydrogenase, type 2 [Source:HGNC Symbol;Acc:32389]

Sequence

>retro_pabe_2891
GACATTAATGAGTCCAAACTTCAGGAACTGGAAAAGTACCTGGGTATTCAAACTCGTGTCCTTGATGTCACAAAGAAGAA
ACAAATTGATCAGTTCGCCAATGAAGTTGAGAGACTTGATGTTCTCTTTAATGTTGCTGGTTTTGTCCATCATGGAACTG
TCCTGGATTGTGAGGAGAAAGACTGGGACTTCTCGATGAATCTCAATGTGCGCAGCATGTACCTGATGATCAAGGCATTC
CTTCCTAAAAATGCTTGCTCAGAAATCTGGCAATATTATCAACATGTCTTCTGTGGCTTCCAGCGTCAAAGGAGTTGTGA
ACAGATGTGTGTACAGCACAACCAAGGCAGCCGTGATTGGCCTCACAAAATCTGTGGCTGCAGATTTCATCCAGCAGGGC
ATCAGGTGCAACTGTGTGTGCCCAGGAACGGTTGATACGCCATCTCTACAAGAAAGAATACAAGCCAGAGGAAATCCTGA
AGAGGCATGGAATGATTTCCTGAAGAGACAAAAGATGGGAAGATTTGCTGCAGAAGAAATAGCCATGCTCTGTGTGTATT
TGGCTTCTGATGAATCTGCTTATGTAACTGGTAACCCTGTCATCACTGATGGAGGATGGAGCTTG

Alignment

ORF - retro_pabe_2891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.14 %
• Parental protein coverage: 85.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DINESKLQELEKYPGIQTRVLDVTKKKQIDQFANEVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNV
          DINESKLQELEKY.GIQTRVLDVTKKKQIDQFANEVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNV
Retrocopy DINESKLQELEKYLGIQTRVLDVTKKKQIDQFANEVERLDVLFNVAGFVHHGTVLDCEEKDWDFSMNLNV

Parental  RSMYLMIKAFLP-KMLAQKSGNIINMSSVASSVKGVVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCV
          RSMYLMIKAFLP.KMLAQKSGNIINMSSVASSVKGVVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCV
Retrocopy RSMYLMIKAFLP>KMLAQKSGNIINMSSVASSVKGVVNRCVYSTTKAAVIGLTKSVAADFIQQGIRCNCV

Parental  CPGTVDTPSLQERIQARGNPEEARNDFLKRQKTGRFATAEEIAMLCVYLASDESAYVTGNPVIIDGGWSL
          CPGTVDTPSLQERIQARGNPEEA.NDFLKRQK.GRFA.AEEIAMLCVYLASDESAYVTGNPVI.DGGWSL
Retrocopy CPGTVDTPSLQERIQARGNPEEAWNDFLKRQKMGRFA-AEEIAMLCVYLASDESAYVTGNPVITDGGWSL

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	0.28 RPM	4.92 RPM
SRP007412_cerebellum	0.49 RPM	4.01 RPM
SRP007412_heart	0.45 RPM	9.15 RPM
SRP007412_kidney	1.66 RPM	50.08 RPM
SRP007412_liver	0.55 RPM	16.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2891 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2891 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3499
Gorilla gorilla	retro_ggor_199

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000164039	1 retrocopy	retro_hsap_3499,
Gorilla gorilla	ENSGGOG00000006381	1 retrocopy	retro_ggor_199,
Pongo abelii	ENSPPYG00000025868	1 retrocopy	retro_pabe_2891 ,
Xenopus tropicalis	ENSXETG00000021320	2 retrocopies	retro_xtro_35, retro_xtro_37,