RetrogeneDB ID: retro_pabe_1039

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:28180533..28182060(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSPPYG00000017824
• Aliases: None
• Description: Lanosterol 14-alpha demethylase [Source:UniProtKB/Swiss-Prot;Acc:Q5RE72]

Sequence

>retro_pabe_1039
ATGGTGGCGGTGGCTGGGATGATGTTGCTGGGCTTGCTGCAGGCGGGGTGGGTCGGTGCTGGGCCAGGCGATGGAGAAGG
TGACAGGCAGCAACCTCTTGTCCATGCTGCTGATCGCCTGCGCCTTCACCCTCAGCCTGGTCTACCTGTTCTGTCTCGCT
GCCGGCCACCTGGTCCAGCTGCCTGCAGGGGCGAAAAGTCCCCCATGCGTTTTCTCCCCAGTTCCATTCCCTGGGCATGC
CATAGCATTTGGGAAAAGTCCAACTGAATTTCTAGAAAATGCATATGAGAAGTATGGACCTGTATTTAGTTTTACCATGG
TAGGCAAGACATTTACTTACCTTCTGGGCAGTGATGCTGCTGCGCTGCTTTTTAATAGTAAAAATTAAGAACTGAATGCA
GAAGATGTCTACAGTCGCCTGACAACACCTGTGTTTGGGAAGGGAGTTGCATGCGATGTGCCTAATCCAGTTTTCTTGGA
GCAGAAGAAAATGTTAAAAAGTGGCCTTAACATAGCCCACTTTAAACAGCATGTTTCTATAATTGAAAAAGAAACAAAGG
AATACTTTCAGAGTTGGGGAGAAAGTGGAGAAAAAATGTGTTTGAAGCTCTTTCTGAGCTCGTAATTTTAACAGCTAGCC
ATTGTTTGCATGGAAAGGAAATCAGAAGTCAACTCAATGAAAAGGTAGCACAGCTGTATGCAGATTTGGATGGAGGTTTC
AGCCATGCAGCCTGGCTCTTACCAGGTTGGCTGCCTTTGCCTAGTTTCAGACGCAGGGACAGAGCTCATCGGGAAATCAA
GGATATTTTCTACAAGGCAATCCAGAAACGCAGACAGTCTCAAGAAAAAATTGATGACATTCTCCAAACTTTACTAGATG
CTACATACAAGGATGGGCATCCTATGACTGATGATGAAGTCGCAGGGATGCTTATTGGATTACTCTTGGCAGGGCAGCAT
ACATCCTCAACTACTAGTGCTTGGATGGGCTTCTTTTTGGCCAGAGACAAAACACTTCAAGAAAAATGTTATTTAGAACA
GAAAACAGTCTGTGGAGAGAATCTGCTTCCTTTAACTTATGACCAGCTCAAGGATCTAAATTTACTTGATCGCTGTATAA
AAGAAACATCAAGACTTAGACCTCCTATAATGATCATGATGAGAATGGCCAGAATTCCTCAGACTGTGGCAGGGTATACC
ATTCCTCCAGGACATCAGGTGTGTGTTTCTCCCACTGTCAATCAAAGACTTAAAGACTCATGGGTAGAACGCCTGGACTT
TAATTCTGATAGCTACTTACAGGATAACCCAGCATCAGGGGAAAAGTTTGCCTACGTGCCATTTGGAGCTGGGCATCATC
GTTGTATTGGGGAAAATTTTGCCTATGTTCAAATTAAGACAATTTGGTCCACTATGCTTCATTTATATGAATTTGATCTC
ATTGATGGATACTTTCCCACTGTGAATTATACAACTATGATTCACACCCCTGAAAACCCAGTTATCCATTACAAACGAAG
ATCAAAA

Alignment

ORF - retro_pabe_1039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAAAGMMLLGLLQAG-GSVLGQAMEKVTGGNLLSMLLIACAFTLSLVYLFRLAVGHLVQLPAGAKSPPY
          M.A.AGMMLLGLLQAG.GSVLGQAMEKVTG.NLLSMLLIACAFTLSLVYLF.LA.GHLVQLPAGAKSPP.
Retrocopy MVAVAGMMLLGLLQAG>GSVLGQAMEKVTGSNLLSMLLIACAFTLSLVYLFCLAAGHLVQLPAGAKSPPC

Parental  IFSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSR
          .FSP.PF.GHAIAFGKSP.EFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKN..LNAEDVYSR
Retrocopy VFSPVPFPGHAIAFGKSPTEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKN*ELNAEDVYSR

Parental  LTTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFESWGESGEK-NVFEALSELI
          LTTPVFGKGVA.DVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYF.SWGESGEK.NVFEALSEL.
Retrocopy LTTPVFGKGVACDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFQSWGESGEK<NVFEALSELV

Parental  ILTASHCLHGKEVRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRR
          ILTASHCLHGKE.RSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRR
Retrocopy ILTASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRR

Parental  QSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQK
          QSQEKIDDILQTLLDATYKDG.P.TDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQK
Retrocopy QSQEKIDDILQTLLDATYKDGHPMTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQK

Parental  TVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLK
          TVCGENL.PLTYDQLKDLNLLDRCIKET.RLRPPIMIMMRMAR.PQTVAGYTIPPGHQVCVSPTVNQRLK
Retrocopy TVCGENLLPLTYDQLKDLNLLDRCIKETSRLRPPIMIMMRMARIPQTVAGYTIPPGHQVCVSPTVNQRLK

Parental  DSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTV
          DSWVERLDFN.D.YLQDNPASGEKFAYVPFGAG.HRCIGENFAYVQIKTIWSTML.LYEFDLIDGYFPTV
Retrocopy DSWVERLDFNSDSYLQDNPASGEKFAYVPFGAGHHRCIGENFAYVQIKTIWSTMLHLYEFDLIDGYFPTV

Parental  NYTTMIHTPENPVIRYKRRSK
          NYTTMIHTPENPVI.YKRRSK
Retrocopy NYTTMIHTPENPVIHYKRRSK

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	34.61 RPM
SRP007412_cerebellum	0.00 RPM	30.52 RPM
SRP007412_heart	0.00 RPM	22.91 RPM
SRP007412_kidney	0.00 RPM	36.59 RPM
SRP007412_liver	0.00 RPM	60.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1039 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1039 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005722	1 retrocopy	retro_amel_1512,
Homo sapiens	ENSG00000001630	2 retrocopies	retro_hsap_1248, retro_hsap_2807,
Loxodonta africana	ENSLAFG00000000066	1 retrocopy	retro_lafr_272,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436,
Pongo abelii	ENSPPYG00000017824	2 retrocopies	retro_pabe_1039 , retro_pabe_1040,
Pan troglodytes	ENSPTRG00000019391	2 retrocopies	retro_ptro_1901, retro_ptro_859,
Tarsius syrichta	ENSTSYG00000014341	1 retrocopy	retro_tsyr_1008,