RetrogeneDB ID: retro_ptro_859

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:28329245..28330210(-)
• 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_859
TACTTTCAGAGTTGGGGAGAAAGTGGAGAAAAAAATGTGTTTGAAGCTCTTTCTGAGCTCATAATTTTAACAGCTAGCCA
CTGTTTGCATGGAAAGGAAATCAGAAGTTAACTCAATGAAAAGGTAGCACAGCTGTATGCAGATTTGGATGGAGGTTTCA
GCCATGCAGCCTGGCTCTTACCAGGTTGGCTGCCTTTGCCTAGTTTCAGATGCAGGGAAAGAGCTCATTGGGAAATCAAG
GATATTTTCTATAAGGCAATCCAGAAACGCAGACAGTCTCAAGAAAAAATTGATGACATTCTCCAAACTTTACTAGATGC
TACATACAAGGATGGGCGTCCTTTGACTGATGATGAAGTAGCAGGGATGCTTATTGGATTACTCTTGGCAGGGCAGCATT
CATCCTCAACTACTAATGCTTGGATGGACTTCTTTTTGGCCAGAGACAAAACACTTCAAAAAAGTGTTATTTAGAACAGA
AAACAGTCTGTGGAGAGAATCTGCCTCCTTTAACTTATGACCAACTCAAGGATCTAAATTTACTTGATCGCTGTATAAAA
GAAACATTAAGACTTAGACCTCCTATAATGATTATGATGAGAATGGCCAGAACTCCTCAGACTGTGGTAGGGTATACCAT
TCCTCCAGGACATCAGGTGTGTGTTTCTCCCACTGTCAATCAAAGACTTAAAGACTCATGGGTAGAACGCCTGGACTTTA
ATCCTGATTGCTACTTACAGGATAACCCAGCATCAGGGGAAAAGTTTGCCTATGTGCCATTTGGAGCTGGGTGTCATCGT
TGAATTGGGGAAAATTTTGCCTATGTTCAAATTAAGACAATTTGGTCCACTATGCTTCGTTTATATGAATTTGATCTCAT
TGATGGATATTTTCCCATCGTGAATTATACAACTATGATTCACACCCCTGAAAACCCACTTATCCATTACAAACAAAGAT
CAAAA

Alignment

ORF - retro_ptro_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 63.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YFQSWGESGEKNVFEALSELIILTASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFR
          YFQSWGESGEKNVFEALSELIILTASHCLHGKEIRS.LNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFR
Retrocopy YFQSWGESGEKNVFEALSELIILTASHCLHGKEIRS*LNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFR

Parental  RRDRAHREIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSA
          .R.RAH.EIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQH.SSTT.A
Retrocopy CRERAHWEIKDIFYKAIQKRRQSQEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHSSSTTNA

Parental  WMGFFLARDKTLQE-KCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTV
          WM.FFLARDKTLQ..KCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTV
Retrocopy WMDFFLARDKTLQK<KCYLEQKTVCGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTV

Parental  AGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIK
          .GYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPD.YLQDNPASGEKFAYVPFGAG.HR.IGENFAYVQIK
Retrocopy VGYTIPPGHQVCVSPTVNQRLKDSWVERLDFNPDCYLQDNPASGEKFAYVPFGAGCHR*IGENFAYVQIK

Parental  TIWSTMLRLYEFDLIDGYFPTVNYTTMIHTPENPVIRYKRRSK
          TIWSTMLRLYEFDLIDGYFP.VNYTTMIHTPENP.I.YK.RSK
Retrocopy TIWSTMLRLYEFDLIDGYFPIVNYTTMIHTPENPLIHYKQRSK

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	0.07 RPM	18.18 RPM
SRP007412_heart	0.06 RPM	7.72 RPM
SRP007412_kidney	0.03 RPM	20.35 RPM
SRP007412_liver	0.07 RPM	33.85 RPM
SRP007412_testis	0.53 RPM	109.49 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_859 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_859 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_859 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1248

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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,