RetrogeneDB ID: retro_ggor_958

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:73064905..73065734(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSGGOG00000001180
• Aliases: None
• Description: None

Sequence

>retro_ggor_958
TTTCCAGGATGGATTGATAACTTTAATGGACCAAGTGGTCTCTTTATTGTGGCAGGGAAAGGAATTCTTTGAACAATGCG
TGTCTCCAATAATGCCCTTGAAGATCTTGTTCCTGTAGATGTAGTTGTCAACAAGAGTCTTGTGGCAGCCTGGTATTCCG
GAGTTAATAGAACAAGAAACCTCATGTCATATAATTGTACAACAGATAGCACTAATCGTTTCCACTGGGGTGAAGTTTAA
TACCATGTGATTTCTACTTTCAAGAGGAATCCTCTCAAACAGGCCTTCAGATGGCCCAATGTGAATCTAACCTCCAATCA
CCTTTTATATCATTCCTTGGATTGCTGTAAGCCATAAGGCCTCAGCATTCCTGAATGATATCTACCTCAGGATGACTGGA
AGAAGCCCAAGGATGATGAAAACAATAATTCATCTTCACAAAGCTGTGATGTTACTTGAGTATTTCACAAGTAATTCTTG
GGTTTGGAATACTGACAATGTCAATATGTTAATGAATCAACTAAACCTTGAAGATAAAAAGACTTTCAATATTGATGTAC
GGCAGTTACATTAGGCACAATATATAGAGAACTACTGCATGGGAACTGAGAAGTACATATTGAATAAAGAAACGTCTGGC
CTCCCTGCAGTCAGAAAACATCTGAACAAGTTGCATAATATACCTTATGATTTTAATACTATCCTTGTGATTCTCATCTG
ACACATTTTTATTGCAAGACCACAAATGGCAAGAAACATCTGATACCTTGTGGTTAGTCTGTGTTACAAGTTTCTGTCAT
AGTTTCAAGCATCCAGCACTATGAGATAC

Alignment

ORF - retro_ggor_958 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.48 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

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

Parental  TNPFHWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHY-WIAVSHKAPAFLYDIYLRMTGRSPRMM
          TN.FHWGEV.YHVISTFKRNPL.QAFR.PNVNLTSNHLLYH..WIAVSHKA.AFL.DIYLRMTGRSPRMM
Retrocopy TNRFHWGEV*YHVISTFKRNPLKQAFRWPNVNLTSNHLLYHS>WIAVSHKASAFLNDIYLRMTGRSPRMM

Parental  KTITRLHKAMVFLEYFTSNSWVWNTDNVNMLMNQLNPEDKKTFNIDVRQLHWAEYIENYCLGTKKYVLNE
          KTI..LHKA...LEYFTSNSWVWNTDNVNMLMNQLN.EDKKTFNIDVRQLH.A.YIENYC.GT.KY.LN.
Retrocopy KTIIHLHKAVMLLEYFTSNSWVWNTDNVNMLMNQLNLEDKKTFNIDVRQLH*AQYIENYCMGTEKYILNK

Parental  EMSGLPAARKHLNKLRNIRYGFNTILVILIWRIFIARSQMARNIWYFVVSLCYKFLSYFRASSTMRY
          E.SGLPA.RKHLNKL.NI.Y.FNTILVILI..IFIAR.QMARNI.Y.VVSLCYKFLS.F.ASSTMRY
Retrocopy ETSGLPAVRKHLNKLHNIPYDFNTILVILI*HIFIARPQMARNI*YLVVSLCYKFLS*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	29.06 RPM
SRP007412_cerebellum	0.00 RPM	44.44 RPM
SRP007412_heart	0.00 RPM	6.94 RPM
SRP007412_kidney	0.00 RPM	27.40 RPM
SRP007412_liver	0.05 RPM	11.00 RPM
SRP007412_testis	0.00 RPM	66.93 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_958 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_958 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1225
Pan troglodytes	retro_ptro_840
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,