RetrogeneDB ID: retro_ggor_33

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:39239652..39241206(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000013340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ENSG00000111275
• Ensembl ID: ENSGGOG00000007108
• Aliases: None
• Description: None

Sequence

>retro_ggor_33
ATGCTGCGCTTCCTGGTACCCCGGCTGCTTAGCCTCCAGGGCAGGACCGCCCGCTACTCCTCGGCAGCAGCCCTCCCAAG
CCCCATTCTGAACCCAGACATCCCCTACAACCAGCTGTTCATCAACAATGAATGGCAAGATGCAGTCAGCAAGAAGACCT
TCCCAACGGTCAACCCTACCACCGGGGAGGTCATCGGGCACGTGGCTGAAGGTGACCGGGCTGATGTGGATCGGGCTGTG
AAAGCAGCCCGGGAAGCCTTCCGCCTGGGGTCTCCATGGCGCCAGATGGATGCCTCTGAGCGGGGCCGGCTGCTGAACCG
CCTGGCAGACCTAGTGGAGCGGGATCGAGTCTACTTGGCCTCACTGGAGACCTTGGACAATGGGAAGCCTTTCCAAGAGT
CTTACGCCTTGGACTTGGATGAGGTCATCAAGGTGTATCGGTACTTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACC
ATCCCCGTGGATGGCCAGCATTTCTGCTTCACCCGGCATGAGCCCGTTGGTGTCTGTGGCCAGATCATCCCGTGGAACTT
CCCCTTGGTCATGCAGGGTTGGAAACTTGCCCCGGCACTCGCCACAGGCAACACTGTGGTTATGAAGGTGGCAGAGCAGA
CCCCCCTCTCTGCCCTGTATTTGGCTTCCCTCATCAAGGAGGCAGGCTTTCCCCCTGGGGTGGTGAACATCATCACGGGC
TATGGCCCAACAGCAGGTGCGGCCATCGCCCAGCACATGGATGTTGACAAAGTTGCCTTCACCGGTTCCACCGAGGTGGG
CCACCTGATCCAGAAAGCAGCTGGCGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGTAAGAGCCCCAGCATTG
TGCTGGCCGATGCTGACATGGAGCATGCCGTGGAGCAGTGCCACGAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGT
GCTGGCTCCCGGACCTTCGTGGAAGAATCCATCTACAATGAGTTTCTCGAGAGAACCGTGGAGAAAGCAAAGCAGAGGAA
AGTGGGGAACCCCTTTGAGCTGGACACCCAGCAGGGGCCTCAGGTGGACAAGGAGCAGTTTGAACAAGTCCTAGGCTACA
TCCAGCTTGGCCAGAAGGAGGGCACAAAACTCCTCTGTGGCGGAGAGCGTTTCGGGGAGCGTGGTTTCTTCATCAAGCCT
ACTGTCTTTGGTGGCGTGCAGGATGACATGAGAATTGCCAAAGAGGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTT
CAAGAAGATTGAGGAGGTGATTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCAGCTGTGTTCACCCGGGATCTGG
ACAAGGCCATGTACTTCACCCAGGCACTTCAGGCCGGGACCGTGTGGGTAAACACCTACAACATCGTCACCTGCCACACG
CCATTTGGAGGGTTTAAGGAATCTGGAAACGGGAGGGAGCTGGGTGAGGATGGGCTTAAGGCCTACACAGAGGTGAAGAC
AGTCACCATCAAGGTTCCTCAGAAGAACTCGTAA

Alignment

ORF - retro_ggor_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 96.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATQAVPAPNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAAQAAFQL
          ....A.P.P...P....NQ.FINNEW.DAVS.KTFPTVNP.TGEVI..VAEGD..DVD.AVKAA..AF.L
Retrocopy SSAAALPSPILNPDIPYNQLFINNEWQDAVSKKTFPTVNPTTGEVIGHVAEGDRADVDRAVKAAREAFRL

Parental  GSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK
          GSPWR.MDAS.RGRLLNRLADL.ERDR.YLA.LETLDNGKP...SY..DLD.V.K..RY.AGWADK.HGK
Retrocopy GSPWRQMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYALDLDEVIKVYRYFAGWADKWHGK

Parental  TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAG
          TIP.DG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKVAEQTPL.ALY.A.LIKEAG
Retrocopy TIPVDGQHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKVAEQTPLSALYLASLIKEAG

Parental  FPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSPNIIMSDAD
          FPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTE.G..IQ.AAG.SNLKRVTLELGGKSP.I...DAD
Retrocopy FPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSNLKRVTLELGGKSPSIVLADAD

Parental  MDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKK
          M..AVEQ.H.ALFFN.GQCCCAGSRTFV.E.IY.EF.ER.V..AK.R.VGNPF...T.QGPQVD..QF..
Retrocopy MEHAVEQCHEALFFNMGQCCCAGSRTFVEESIYNEFLERTVEKAKQRKVGNPFELDTQQGPQVDKEQFEQ

Parental  ILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVLDGMTIAKEEIFGPVMQILKFKTIEEVVGRANN
          .LGYI..G..EG.KLLCGG.....RG.FI.PTVFG.V.D.M.IAKEEIFGPV....KFK.IEEV..RANN
Retrocopy VLGYIQLGQKEGTKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGPVQPLFKFKKIEEVIERANN

Parental  STYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVT
          ..YGLAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SG.GRELGE.GL.AYTEVKTVT
Retrocopy TRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGNGRELGEDGLKAYTEVKTVT

Parental  VKVPQKNS
          .KVPQKNS
Retrocopy IKVPQKNS

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	14.48 RPM	205.58 RPM
SRP007412_cerebellum	11.62 RPM	137.03 RPM
SRP007412_heart	8.60 RPM	135.68 RPM
SRP007412_kidney	29.44 RPM	607.45 RPM
SRP007412_liver	42.84 RPM	1053.17 RPM
SRP007412_testis	18.13 RPM	206.68 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_33 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_33 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_19
Pan troglodytes	retro_ptro_118
Pongo abelii	retro_pabe_32
Macaca mulatta	retro_mmul_247
Mus musculus	retro_mmus_222
Rattus norvegicus	retro_rnor_307
Bos taurus	retro_btau_48
Sus scrofa	retro_sscr_9

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013664	1 retrocopy	retro_amel_51,
Bos taurus	ENSBTAG00000008743	1 retrocopy	retro_btau_48,
Canis familiaris	ENSCAFG00000008683	1 retrocopy	retro_cfam_1493,
Equus caballus	ENSECAG00000017673	2 retrocopies	retro_ecab_1054, retro_ecab_1061,
Felis catus	ENSFCAG00000022000	1 retrocopy	retro_fcat_1590,
Homo sapiens	ENSG00000111275	1 retrocopy	retro_hsap_19,
Gorilla gorilla	ENSGGOG00000007108	1 retrocopy	retro_ggor_33 ,
Latimeria chalumnae	ENSLACG00000011798	1 retrocopy	retro_lcha_108,
Microcebus murinus	ENSMICG00000003487	1 retrocopy	retro_mmur_19,
Myotis lucifugus	ENSMLUG00000017084	1 retrocopy	retro_mluc_1918,
Macaca mulatta	ENSMMUG00000008336	1 retrocopy	retro_mmul_247,
Mustela putorius furo	ENSMPUG00000002282	1 retrocopy	retro_mputfur_27,
Mus musculus	ENSMUSG00000029455	1 retrocopy	retro_mmus_222,
Nomascus leucogenys	ENSNLEG00000000016	1 retrocopy	retro_nleu_22,
Otolemur garnettii	ENSOGAG00000033093	1 retrocopy	retro_ogar_203,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pteropus vampyrus	ENSPVAG00000013189	1 retrocopy	retro_pvam_163,
Rattus norvegicus	ENSRNOG00000001344	1 retrocopy	retro_rnor_307,
Sus scrofa	ENSSSCG00000009889	1 retrocopy	retro_sscr_9,
Ictidomys tridecemlineatus	ENSSTOG00000015009	1 retrocopy	retro_itri_33,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,