RetrogeneDB ID: retro_ptro_840

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:90314991..90315819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSPTRG00000024190
• Aliases: FAR1, MLSTD2
• Description: None

Sequence

>retro_ptro_840
TTTCCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTTATTGTGGCAGGGAAAGGAATTATTTGAACAATGCG
TGTCTCCAATAATGCCCTTGAAGATCTTGTTCCTGTAGATGTAGTTGTCAACAAGAGTCTTGTGGCAGCCTGGTATTCTG
GAGTTAATAGAACAAGAAACCTCATGTCATATAATTGTACAACAGATAGCACTAATCATTTCCACTGGGGTGACGTTTAA
TACCATGTAATTTCTACTTTCAAGAGGAATCTTCTCGAACAGGCCTTCAGATGGCCCAATGTAAATCTAACCTCCAATCA
CCTTTTATATCATTACTGGATTGCCGTAAGCCATAAGGCCTCAGCATTCCTGGATGATATCTACCTCAGGATGACTGGAA
GAAACCCAAGGATGATGAAAACAATAATTCATCTTCACAAAGCTGTGATGTTACTTGAGTATTTCACAAGTAATTCTTGG
GTTTGGAATACTGACAATGTCAATATGTTAATGAATCAACTAAACCTTGAAGATAAAAAGACTTTCAATATTGATGTACG
GCAGTTACATTAGGCAGAATATATAGAGAACTCCTGCATGGGAACTGAGAAGTACATATTGAATAAAGAAACGTCTGGCC
TCCCTGCAGTCAGAAAACATCTGAACAAGTTGCGTAATATACCTTATGATTTTAATACTATCCTTGTGATCCTCATCTGA
CACATTTTTATTGCAAGACCACAAATGGCAAGAAACATCTGATACTTTGTGGTTAGTCTGTGTTACAAGTTTCTGTCATA
GTTTCAAGCATCCAGCACTATGAGATAC

Alignment

ORF - retro_ptro_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPGWIDNFNGPSGLFIAAGKGILRTIRASNNALADLVPVDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGS
          FPGWIDNFNGPSGLFI.AGKGI..T.R.SNNAL.DLVPVDVVVN.SL.AAWYSGVNR.RN.M.YNCTT.S
Retrocopy FPGWIDNFNGPSGLFIVAGKGII*TMRVSNNALEDLVPVDVVVNKSLVAAWYSGVNRTRNLMSYNCTTDS

Parental  TNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHYWIAVSHKAPAFLYDIYLRMTGRSPRMMK
          TN.FHWG.V.YHVISTFKRN.LEQAFR.PNVNLTSNHLLYHYWIAVSHKA.AFL.DIYLRMTGR.PRMMK
Retrocopy TNHFHWGDV*YHVISTFKRNLLEQAFRWPNVNLTSNHLLYHYWIAVSHKASAFLDDIYLRMTGRNPRMMK

Parental  TITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPEDKKTFNIDVRQLHWAEYIENYCLGTKKYVLNEE
          TI..LHKA...LEYFTSNSWVWNTDNVNMLMNQLN.EDKKTFNIDVRQLH.AEYIEN.C.GT.KY.LN.E
Retrocopy TIIHLHKAVMLLEYFTSNSWVWNTDNVNMLMNQLNLEDKKTFNIDVRQLH*AEYIENSCMGTEKYILNKE

Parental  MSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNIWYFVVSLCYKFLSYFRASSTMRY
          .SGLPA.RKHLNKLRNI.Y.FNTILVILI..IFIAR.QMARNI.YFVVSLCYKFLS.F.ASSTMRY
Retrocopy TSGLPAVRKHLNKLRNIPYDFNTILVILI*HIFIARPQMARNI*YFVVSLCYKFLS*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	48.98 RPM
SRP007412_cerebellum	0.00 RPM	52.98 RPM
SRP007412_heart	0.00 RPM	29.99 RPM
SRP007412_kidney	0.00 RPM	28.71 RPM
SRP007412_liver	0.00 RPM	3.57 RPM
SRP007412_testis	1.05 RPM	35.41 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_840 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_840 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1225
Gorilla gorilla	retro_ggor_958
Pongo abelii	retro_pabe_1019
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,