RetrogeneDB ID: retro_pabe_1105

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:41730300..41730572(+)
• Located in intron of: ENSPPYG00000005771

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSPPYG00000012604
• Aliases: None
• Description: FK506 binding protein 1B, 12.6 kDa [Source:HGNC Symbol;Acc:3712]

Sequence

>retro_pabe_1105
AAGAAGAGCCAGATGTGTGTAGCACACTACATAGGGATGTTCCAAAATGGGGATAGATTTGATTTATCCCAAGACAGAAA
CAAACCTTTCAAGTTCAAAACTGGTGAACAGGAAGTCATCAATGGTTTTGAAGAGTACCTAGCACAGATGAGCTTGGGGC
AGAAGGTGAAGCTGACCTGCATACATGATGTGTCATATAGAGCTCCAGGCTACTCTAGTGTCATCCCTCCCAGTGCTACC
CTATCTTTGACATGGAACTGCTCAACTTAGAG

Alignment

ORF - retro_pabe_1105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.57 %
• 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.HY.GM.QNG..FD.S.DRNKPFKF..G.QEVI.GFEE..AQMSLGQ..KLTC..DV.Y.A.G
Retrocopy KKSQMCVAHYIGMFQNGDRFDLSQDRNKPFKFKTGEQEVINGFEEYLAQMSLGQKVKLTCIHDVSYRAPG

Parental  HPGVIPPNATL-IFDVELLNLE
          ...VIPP.ATL.IFD.ELLNLE
Retrocopy YSSVIPPSATL<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	0.06 RPM	25.60 RPM
SRP007412_cerebellum	0.00 RPM	40.37 RPM
SRP007412_heart	0.00 RPM	0.72 RPM
SRP007412_kidney	0.00 RPM	1.13 RPM
SRP007412_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1105 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1105 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1105 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1329
Pan troglodytes	retro_ptro_906
Gorilla gorilla	retro_ggor_1036
Macaca mulatta	retro_mmul_2171
Callithrix jacchus	retro_cjac_696

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007700	1 retrocopy	retro_cjac_696,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Equus caballus	ENSECAG00000015664	1 retrocopy	retro_ecab_752,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Macaca mulatta	ENSMMUG00000012341	1 retrocopy	retro_mmul_2171,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
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	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,