RetrogeneDB ID: retro_pabe_1019

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:92140341..92141167(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSPPYG00000003470
• Aliases: FAR1, MLSTD2
• Description: Fatty acyl-CoA reductase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R834]

Sequence

>retro_pabe_1019
TTTCCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTTGTTGTGGCAGGGAAAGGAATTCTTTGAACAATGCG
TGTCTCCAATAATGCCCTTGAAGATCTTGTTCCTGTAGATGTAGTTGTCAACAAGAGTCTTGTGGCAGCCTGGTATTCCA
GAGTTAATAGCACAAGAAACCTCATGTCATATAATTGTACAACAGATAGCACTAATCCTTTCCACTGGGGTGAAGTTTAA
TACCATGTGATTTCTACTTTCAAGAGGAATCCTCATGAACAGGCCTTCAGATGGCCCAATGTAAATCTAACCTCCAATCA
CCTTTTATATCATTACTGGATTGCCGTAAGCCATAAGGCCTCAGCATTCCTGGATGATATCTATCTCAGGATGACTGGAA
GAAGCCCAAGGATGATGAAAACAATAACTCATCTTCACAAAGCTGTAATGTTACTTGAGTATTTCACAAGTAATCCTTGG
GTTTGGAATACTGACAGTGTCAATATGTTAATGAATCAACTAAACCTTGAAGATAAAAAGACTTTCAATATTGATGTACG
GCAGTTACGTTAGGCAGAATATATGGAGAACTACTGCATGGGAACTGAGAAGTACATTTTGAATAAAGAAACGTCTGGCC
TCCCTGCAGTCAGAAAACATCTGAACAAGTTGCATAATATATCTTATGATTTTAATACTATCCTTGTGATCCTCATCTGA
CACATTTTTATTGCAAGACCACAAATGGCAAGAAACGTGATACTTTGTGGTTAGTCTGTGTTACAAGTTTCTGTCATAGT
TTCAAGCATCCAGCACTATGAGATAC

Alignment

ORF - retro_pabe_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.31 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FPGWIDNFNGPSGLFIAAGKGILRTIRASNNALADLVPVDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGS
          FPGWIDNFNGPSGLF..AGKGIL.T.R.SNNAL.DLVPVDVVVN.SL.AAWYS.VN..RN.M.YNCTT.S
Retrocopy FPGWIDNFNGPSGLFVVAGKGIL*TMRVSNNALEDLVPVDVVVNKSLVAAWYSRVNSTRNLMSYNCTTDS

Parental  TNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHYWIAVSHKAPAFLYDIYLRMTGRSPRMMK
          TNPFHWGEV.YHVISTFKRNP.EQAFR.PNVNLTSNHLLYHYWIAVSHKA.AFL.DIYLRMTGRSPRMMK
Retrocopy TNPFHWGEV*YHVISTFKRNPHEQAFRWPNVNLTSNHLLYHYWIAVSHKASAFLDDIYLRMTGRSPRMMK

Parental  TITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPEDKKTFNIDVRQLHWAEYIENYCLGTKKYVLNEE
          TIT.LHKA...LEYFTSN.WVWNTD.VNMLMNQLN.EDKKTFNIDVRQL..AEY.ENYC.GT.KY.LN.E
Retrocopy TITHLHKAVMLLEYFTSNPWVWNTDSVNMLMNQLNLEDKKTFNIDVRQLR*AEYMENYCMGTEKYILNKE

Parental  MSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNI-WYFVVSLCYKFLSYFRASSTMRY
          .SGLPA.RKHLNKL.NI.Y.FNTILVILI..IFIAR.QMARN.....V.SLCYKFLS.F.ASSTMRY
Retrocopy TSGLPAVRKHLNKLHNISYDFNTILVILI*HIFIARPQMARNV>YFVV-SLCYKFLS*FQASSTMRY

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	29.47 RPM
SRP007412_cerebellum	0.00 RPM	94.36 RPM
SRP007412_heart	0.00 RPM	23.96 RPM
SRP007412_kidney	0.00 RPM	24.40 RPM
SRP007412_liver	0.00 RPM	7.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1019 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1019 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1225
Pan troglodytes	retro_ptro_840
Gorilla gorilla	retro_ggor_958
Macaca mulatta	retro_mmul_1301

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019 ,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,