RetrogeneDB ID: retro_pabe_1040

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:28184814..28185915(-)
• 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_1040
CCTGTGTTTGGGAAGGGAGTTGCATGCGATGTGCTAATCCAGGTGTCTTGGAGCAGAAGAAAATGTAAAAAAGTGACTTT
AACATAGCCCACTTTAAACAGCATGTTCCCATAATTGAAAAAGAAACAAAGGAATACTTTTCAGAGTTGGGGAGAAAGTG
GAGAAAAAAATGTGTTTGAAGCTCTTTCTGAGCTCGTAATTTTAACAGCTAGCCATTGTTTGCATGGAAAGGAAATCAGA
AGTCAACTCAATGAAAAGGTAGCACAGCTGTATGCAGATTTGGATGGAGGTTTCAGCCATGCAGCCTGGCTCTTACCAGG
TTGGCTGCCTTTGCCTAGTTTCAGACGCAGGGACAGAGCTCATCGGGAAATGAAGGATATTTTCTACAAGGCAATCCAGA
AACGCAGACAGTCTCAAGAAAAAATTGATGACATTCTCCAAACTTTACTAGATGCTACATACAAGGATGGGCATCCTATG
ACTGATGATGAAGTGGCAGGGATGCTTATTGGATTACTCTTGGCAGGGCAGCATACATCCTCAACTACTAGTGCTTGGAT
GGGCTTCTTTTTGGCCAGAGACAAAACACTTCAAGAAAAATGTTATTTAGAAGAGAAAACAGTCTGTGGAGAGAATCTGC
TTCCTTTAACTTATGACCAGCTCAAGGATCTAAATTTACTTGATCGCTGTATAAAAGAAACATCAAGACTTAGACCTCCT
ATAATGATCATGATGAGAATGGCCAGAATTCCTCAGACTGTGGCAGGGTATACCATTCCTCCAGGACATCAGGTGTGTGT
TTCTCCCACTGTCAATCAAAGACTTAAAGACTCATGGGTAGAACGCCTGGACTTTAATTCTGATAGCTACTTACAGGATA
ACCCAGCATCAGGGGAGAAGTTTGCCTATGTGCCATTTGGAGCTGGGCATCATCGTTGTATTGGGGAAAATTTTGCCTAT
GTTCAAATTAAGACAATTTGGTCCACTATGCTTCATTTATATGAATTTGATCTCATTGATGGATACTTTCCCACCGTGAA
TTATACAACTATGATTCACACCCCTGAAAACCCAGTTATCCATTACAAACGAAGATCAAAA

Alignment

ORF - retro_pabe_1040 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.22 %
• Parental protein coverage: 72.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVFGKGVAYDV-PNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYF-ESWGESGEKNVFEALSELIIL
          PVFGKGVA.DV..NP..LEQKKM.KS..NIAHFKQHV.IIEKETKEYF..SWGESGEKNVFEALSEL.IL
Retrocopy PVFGKGVACDV<ANPGVLEQKKM*KSDFNIAHFKQHVPIIEKETKEYF>QSWGESGEKNVFEALSELVIL

Parental  TASHCLHGKEVRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQS
          TASHCLHGKE.RSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHRE.KDIFYKAIQKRRQS
Retrocopy TASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREMKDIFYKAIQKRRQS

Parental  QEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQKTV
          QEKIDDILQTLLDATYKDG.P.TDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLE.KTV
Retrocopy QEKIDDILQTLLDATYKDGHPMTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEEKTV

Parental  CGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDS
          CGENL.PLTYDQLKDLNLLDRCIKET.RLRPPIMIMMRMAR.PQTVAGYTIPPGHQVCVSPTVNQRLKDS
Retrocopy CGENLLPLTYDQLKDLNLLDRCIKETSRLRPPIMIMMRMARIPQTVAGYTIPPGHQVCVSPTVNQRLKDS

Parental  WVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNY
          WVERLDFN.D.YLQDNPASGEKFAYVPFGAG.HRCIGENFAYVQIKTIWSTML.LYEFDLIDGYFPTVNY
Retrocopy WVERLDFNSDSYLQDNPASGEKFAYVPFGAGHHRCIGENFAYVQIKTIWSTMLHLYEFDLIDGYFPTVNY

Parental  TTMIHTPENPVIRYKRRSK
          TTMIHTPENPVI.YKRRSK
Retrocopy TTMIHTPENPVIHYKRRSK

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	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_1040 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1040 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1040 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,