RetrogeneDB ID: retro_ptro_2983

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL390389.1:3410128..3410452(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000023826
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP1A
• Ensembl ID: ENSPTRG00000013163
• Aliases: None
• Description: Peptidyl-prolyl cis-trans isomerase [Source:UniProtKB/TrEMBL;Acc:H2QJT5]

Sequence

>retro_ptro_2983
ATGGGAGTGCACGTGGAAACCATCTCCCCAGGAGACTGGCGCACCTTCCCGAAGCGCAGCCAGACCTGCGTGATGCACTA
CACCGGGATGCTTGAAGATAGAAAGAAATTTGATTCCTCCCGGGATAGAAACAAGCCCTTTAAGTTTATGCTAGGCAAGC
AGGAGGTGATCCGAGGCTGGGAAGAAGAGGTTGCCCAGATGAGTGTGGGTCAGAGAGCCAAACTGACTATATCTCCAGAT
TATGCCTATGGTGCCACTGGGCACCCAGGCATCATCCCACCACATGCCACTCTCGTCTTCGATGTGGAGCTTCTAAAACT
GGAA

Alignment

ORF - retro_ptro_2983 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVG
          MGV.VETISPGD.RTFPKR.QTCV.HYTGMLED.KKFDSSRDRNKPFKFMLGKQEVIRGWEE.VAQMSVG
Retrocopy MGVHVETISPGDWRTFPKRSQTCVMHYTGMLEDRKKFDSSRDRNKPFKFMLGKQEVIRGWEEEVAQMSVG

Parental  QRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
          QRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Retrocopy QRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE

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	1.04 RPM	168.25 RPM
SRP007412_cerebellum	0.00 RPM	41.66 RPM
SRP007412_heart	0.09 RPM	47.33 RPM
SRP007412_kidney	0.08 RPM	89.83 RPM
SRP007412_liver	0.07 RPM	48.02 RPM
SRP007412_testis	0.11 RPM	44.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2983 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2983 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2344

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008303	4 retrocopies	retro_btau_1220, retro_btau_1265, retro_btau_128, retro_btau_1760,
Callithrix jacchus	ENSCJAG00000020908	4 retrocopies	retro_cjac_1544, retro_cjac_3889, retro_cjac_4157, retro_cjac_537,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Homo sapiens	ENSG00000088832	1 retrocopy	retro_hsap_1198,
Gorilla gorilla	ENSGGOG00000001729	3 retrocopies	retro_ggor_1494, retro_ggor_2344, retro_ggor_933,
Macaca mulatta	ENSMMUG00000015996	1 retrocopy	retro_mmul_10,
Monodelphis domestica	ENSMODG00000019554	2 retrocopies	retro_mdom_151, retro_mdom_733,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654, retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
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,
Sus scrofa	ENSSSCG00000007188	1 retrocopy	retro_sscr_98,
Tursiops truncatus	ENSTTRG00000003547	3 retrocopies	retro_ttru_1227, retro_ttru_802, retro_ttru_904,
Vicugna pacos	ENSVPAG00000011511	1 retrocopy	retro_vpac_171,