RetrogeneDB ID: retro_pabe_1654

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:60005076..60005400(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1A
• Ensembl ID: ENSPPYG00000010852
• Aliases: None
• Description: FK506 binding protein 1A, 12kDa [Source:HGNC Symbol;Acc:3711]

Sequence

>retro_pabe_1654
ATGGGAGTGCAGGTGGAAACCATCTCCCCAGGAGAGGAGCGCACCTTCCTGAGGCAAGGCCAGACCTGCATGGTGCACTA
CACCCGGATGCTTGAATATGGAAAGAAATTTGATTCCTCCCGGGACAGAAACAACCCCTTTAATTTTATGCTAGGAAAGC
AGGAGGTGATCCGAGGCTGGGAAGAAAGGGTTGCTTAGATGAGTGTGGGTCAGAGAGCCAAACTGACTATATCTCCAGAT
TCTGCCTATGGTGCCACTGGGCACCCAGGCATCATCCCACCCCATGCCACTCTCGTCTTCATTGTGGAGCTTCTAAAACT
GGAA

Alignment

ORF - retro_pabe_1654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVG
          MGVQVETISPG..RTF...GQTC.VHYT.MLE.GKKFDSSRDRN.PF.FMLGKQEVIRGWEE.VA.MSVG
Retrocopy MGVQVETISPGEERTFLRQGQTCMVHYTRMLEYGKKFDSSRDRNNPFNFMLGKQEVIRGWEERVA*MSVG

Parental  QRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
          QRAKLTISPD.AYGATGHPGIIPPHATLVF.VELLKLE
Retrocopy QRAKLTISPDSAYGATGHPGIIPPHATLVFIVELLKLE

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	176.54 RPM
SRP007412_cerebellum	0.24 RPM	64.69 RPM
SRP007412_heart	0.00 RPM	46.15 RPM
SRP007412_kidney	0.00 RPM	83.66 RPM
SRP007412_liver	0.00 RPM	80.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1654 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1654 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1654 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 34 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,
Otolemur garnettii	ENSOGAG00000002629	1 retrocopy	retro_ogar_673,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pongo abelii	ENSPPYG00000010852	5 retrocopies	retro_pabe_1654 , retro_pabe_1686, retro_pabe_2364, retro_pabe_2365, retro_pabe_998,
Pongo abelii	ENSPPYG00000012604	1 retrocopy	retro_pabe_1105,
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,