RetrogeneDB ID: retro_ptro_906

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 14:40551011..40551283(+)
• Located in intron of: ENSPTRG00000006300

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSPTRG00000011708
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H2QHI6]

Sequence

>retro_ptro_906
AAGAAGAGCCAGATGTGTGTAGCGCAGTACATAGGGGTGTTCCAAAATGGGAATAAATTTGATTTATCCGAAGACAGAAA
CAAACCTTTCAAGTTCAAAACTGGTGAACAGGAAGTCATCAATGGTTTTGAAGAGTACATAGCGCAGATGAGCTTGGGGC
AGAAGGTGAAGCTGACCTGCATATGTGATGTGTCATATAGAGCTCCAGGCTACTCTAGTATCATCCCTCCCAGTGCTACC
CTATCTTTGACATGGAATTGCTCAACTTAGAG

Alignment

ORF - retro_ptro_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.39 %
• Parental protein coverage: 84.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATG
          KK.Q.CV..Y.G..QNG.KFD.S.DRNKPFKF..G.QEVI.GFEE..AQMSLGQ..KLTC..DV.Y.A.G
Retrocopy KKSQMCVAQYIGVFQNGNKFDLSEDRNKPFKFKTGEQEVINGFEEYIAQMSLGQKVKLTCICDVSYRAPG

Parental  HPGVIPPNATL-IFDVELLNLE
          ....IPP.ATL.IFD.ELLNLE
Retrocopy YSSIIPPSATL<IFDMELLNLE

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	0.04 RPM	17.37 RPM
SRP007412_cerebellum	0.04 RPM	6.38 RPM
SRP007412_heart	0.00 RPM	0.38 RPM
SRP007412_kidney	0.00 RPM	1.83 RPM
SRP007412_liver	0.00 RPM	2.16 RPM
SRP007412_testis	0.00 RPM	0.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_906 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_906 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_906 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1329
Gorilla gorilla	retro_ggor_1036
Pongo abelii	retro_pabe_1105
Macaca mulatta	retro_mmul_2171
Callithrix jacchus	retro_cjac_696

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002797	1 retrocopy	retro_amel_1717,
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752,
Erinaceus europaeus	ENSEEUG00000013920	2 retrocopies	retro_eeur_135, retro_eeur_514,
Echinops telfairi	ENSETEG00000018990	2 retrocopies	retro_etel_186, retro_etel_2071,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Microcebus murinus	ENSMICG00000001530	1 retrocopy	retro_mmur_257,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906 ,
Pan troglodytes	ENSPTRG00000013163	2 retrocopies	retro_ptro_2983, retro_ptro_818,
Sorex araneus	ENSSARG00000013808	1 retrocopy	retro_sara_24,
Tupaia belangeri	ENSTBEG00000012282	1 retrocopy	retro_tbel_56,