RetrogeneDB ID: retro_ptro_1901

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:84313864..84315388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSPTRG00000019391
• Aliases: None
• Description: None

Sequence

>retro_ptro_1901
ATGGCGGCGGCGGCCGGGATGATGCTGCTGGGCTTGCTACAGGCGGGTGGGTAGGTGCTGGGCCAGGCGATGGAGGAGGT
AACAGGCGGCAACCTCTTGTCCATGCTGCTGATCGCCTGCGCCTTCACCCTCAGCCTGGTCTACTTGTTCCGTCTCGCCG
CCGGCCACCTGGTCCAGCTGACCGCAGGGGCGAAAAGTCCTCCGTACATTTTCTCCCCAATTCCTTTCCTTGGGCATGCC
ATAGCATTTGGGAAAAGTCCAACTGAATTTCTAGAAAATGCATATGGGAATTATGGACCTGTATTTAGTTTTATCATGGT
AGGCAAGGCATTTACTTACCTTCTGGGGAGTGATGCTGCTGCACTGCTTTTTAATAGTAAAAATGAAGTCCTGAATGCAG
AAGATGTCTACAGTCGCCTGACAACACCTGTGTTTGGGAAGGGAGTTGCTTACGATGTGCCTAATCCAGTTTTCTTGGAG
CAGAAGAAAATGTTAAAAAGTGGCCTTAATATAGCCCATTTTAAAAAGCATGTTTCTATAATTGAAAAAGAAACAAAGGA
ATACTTTGAGAGTTGGGGAGAAAGTGGAGAAAAAAATGTGTTTGCAGCTCTTTCTGAGCTCATAATTTTAACAGCTAGCC
ATTATTTGCATGGAAAGGAAATCAGAAGTCAACCCAATGAAAAGGTAGCACAGCTGTATGCAGATTTGGATGGAGGTTTC
AGCCATGCAGCCTGGCTCTTACCAGGTTGGCTGCCTTTGCCTAGTTTCAGACGCAGGGACAGAGCTCATCGGGAAATCAA
GGATATTTTCTATAAGGCAATCCAGAAACGCAGACAGTCTCAAGAAAAAATTGATGACATTCTCCAAACTTTACTAGATG
CTACATACGAGGATGGGCGTCCTTTGACTGATGATGAAGTAGCAGGGATGCTTATTGGATTACTCTTAGCAGAGCAGCAT
ACAACCTCAACTAGTGCTTAGATGGGCTTCTTTTTGGCCAGAGACAAAACACTTCATGAAAAATGTTATTTAGAACAGAA
AACAGTCTGTGGAGAGAATCTGCCTCCTTTAACTTATGACCAGCTCAAGGATCTAAATTTACTTGATCGCTGTATAAAAG
AAACATTAAGACTTAGACATCCTGTAATGATCATGATGAGAATGGCCAGAATTCCTAAAACTGTGGCAGGGTATACCATT
CCTCCGGGACATCAGGTGTGTGTTTCTCCTACTGTCAATCAAAGACTTAAAGATTCATGGGTAGAACGCCTGGACTTTAA
TCCTGATCGCTACTTATAGGATAACCCAGCATCAAGGGAAAAGTTTGCCTATGTGCCATTTGGAGCTGGGCATCATGGTT
GTATTGGGGAAAATTTTGCCTATGTTCAAATTAAGACAATTTGGTCCACTATGCTTCGTTTATATGAATTTGATCTCATT
GATGGATTCTTTCCCACCGTGAATTATACAACTATGATTCACACCCCTGAAAACCCAGTTATCCATTACAAACGAAGATC
AAAA

Alignment

ORF - retro_ptro_1901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAGMLPLGLLQAGGSVLGQAMEKVTGGNLLSMLLIACAFTLSLVYLFRLAAGHLVQLPAGVKSPPYI
          MAAAAGM..LGLLQAGG.VLGQAME.VTGGNLLSMLLIACAFTLSLVYLFRLAAGHLVQL.AG.KSPPYI
Retrocopy MAAAAGMMLLGLLQAGG*VLGQAMEEVTGGNLLSMLLIACAFTLSLVYLFRLAAGHLVQLTAGAKSPPYI

Parental  FSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRL
          FSPIPFLGHAIAFGKSP.EFLENAY..YGPVFSF.MVGK.FTYLLGSDAAALLFNSKNE.LNAEDVYSRL
Retrocopy FSPIPFLGHAIAFGKSPTEFLENAYGNYGPVFSFIMVGKAFTYLLGSDAAALLFNSKNEVLNAEDVYSRL

Parental  TTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFQSWGESGEKNVFEALSELIIL
          TTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFK.HVSIIEKETKEYF.SWGESGEKNVF.ALSELIIL
Retrocopy TTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKKHVSIIEKETKEYFESWGESGEKNVFAALSELIIL

Parental  TASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQS
          TASH.LHGKEIRSQ.NEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQS
Retrocopy TASHYLHGKEIRSQPNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQS

Parental  QEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQKTV
          QEKIDDILQTLLDATY.DGRPLTDDEVAGMLIGLLLA.QHT.S.TSA.MGFFLARDKTL.EKCYLEQKTV
Retrocopy QEKIDDILQTLLDATYEDGRPLTDDEVAGMLIGLLLAEQHTTS-TSA*MGFFLARDKTLHEKCYLEQKTV

Parental  CGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDS
          CGENLPPLTYDQLKDLNLLDRCIKETLRLR.P.MIMMRMAR.P.TVAGYTIPPGHQVCVSPTVNQRLKDS
Retrocopy CGENLPPLTYDQLKDLNLLDRCIKETLRLRHPVMIMMRMARIPKTVAGYTIPPGHQVCVSPTVNQRLKDS

Parental  WVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNY
          WVERLDFNPDRYL.DNPAS.EKFAYVPFGAG.H.CIGENFAYVQIKTIWSTMLRLYEFDLIDG.FPTVNY
Retrocopy WVERLDFNPDRYL*DNPASREKFAYVPFGAGHHGCIGENFAYVQIKTIWSTMLRLYEFDLIDGFFPTVNY

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	0.07 RPM	19.27 RPM
SRP007412_cerebellum	0.04 RPM	18.18 RPM
SRP007412_heart	0.00 RPM	7.72 RPM
SRP007412_kidney	0.03 RPM	20.35 RPM
SRP007412_liver	0.07 RPM	33.85 RPM
SRP007412_testis	0.32 RPM	109.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1901 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1901 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2807
Gorilla gorilla	retro_ggor_1952

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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,