RetrogeneDB ID: retro_pabe_2429

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:39246702..39247335(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B6
• Ensembl ID: ENSPPYG00000004673
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 6 [Source:HGNC Symbol;Acc:23316]

Sequence

>retro_pabe_2429
CTCTGGAGACTGGTGAACAATGCAGGCATTCTTACACCAATTACCTTATGTGAGTGGCTGAACACTGAGGACTTTATGAA
TATGCTCAAGGTGAACCTCATTGGTGTGATCCAGGTGACCTTGAGCGTGCTTCCTTTGGTGAGGAGAGCACGGGGAAGAA
TTGTCAATGTCTCCAGCATTCTGGGAAGAGTTGCTTTCTTTGTAGAAGGCTACTGTGTCTCCAAGTATGGAGTGGAAGCC
TTTTCAGATATTCTGAGGCGTGAGATTCAACATTTTGGGGTGAAAATCAGCATAGATGAACTTGGCTACTTCAGAACAGG
AATGACAAACCTGACACAGTCCTTAGAGCGAATGAAGCAAAGTTGGAAAGAAGCCCCCAAGCACATTAAGGAGACCTATG
GACAGCATTTTGATGCCTTTTACAGTATCATGAAGGAAGGGCTGTTGAATTGTAGCACAAACCTGAACCTGGTCACTGAC
TGCATGGAACATGCTCTGACATTGGTGCATCCGCAAACTCGATATTCAGCTGGCTGGGATGCTAAATTTTTCTTCATCCC
TCTATCTTATTTACCTACATCACTGGCAGACTACATTTTGACTAGATCTTGGCCCAAACCAGCCCAGGCAGTC

Alignment

ORF - retro_pabe_2429 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.28 %
• Parental protein coverage: 66.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWGLVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLSMLPLVRRARGRIVNVSSILGRVAFFVGG
          LW.LVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLS.LPLVRRARGRIVNVSSILGRVAFFV.G
Retrocopy LWRLVNNAGILTPITLCEWLNTEDFMNMLKVNLIGVIQVTLSVLPLVRRARGRIVNVSSILGRVAFFVEG

Parental  YCVSKYGVEAFSDILRREIQHFGVKISIVEPGYFRTGMTNLTQSLERMKQRWKEAPKHIKETYGQQYFDA
          YCVSKYGVEAFSDILRREIQHFGVKISI.E.GYFRTGMTNLTQSLERMKQ.WKEAPKHIKETYG.Q.FDA
Retrocopy YCVSKYGVEAFSDILRREIQHFGVKISIDELGYFRTGMTNLTQSLERMKQSWKEAPKHIKETYG-QHFDA

Parental  FYSIMKEGLLNCSTNLNLVTDCMEHALTSVHPRTRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ
          FYSIMKEGLLNCSTNLNLVTDCMEHALT.VHP.TRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ
Retrocopy FYSIMKEGLLNCSTNLNLVTDCMEHALTLVHPQTRYSAGWDAKFFFIPLSYLPTSLADYILTRSWPKPAQ

Parental  AV
          AV
Retrocopy AV

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	2.65 RPM
SRP007412_cerebellum	0.00 RPM	1.09 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.40 RPM
SRP007412_liver	0.12 RPM	218.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2429 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2429 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000004673	1 retrocopy	retro_pabe_2429 ,
Tarsius syrichta	ENSTSYG00000013583	1 retrocopy	retro_tsyr_1879,