RetrogeneDB ID: retro_ggor_1455

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:50434403..50435508(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC1B
• Ensembl ID: ENSGGOG00000013186
• Aliases: None
• Description: None

Sequence

>retro_ggor_1455
TCACTGCATCAGTTTTTACTAGAGCCAATCACCTGTCGTGCCTGGAACAGGGATCGTACTGAGATTGCCCTCAGTCCTGA
TAATCAGGAAGCGCACATCTATAAGAAGCACGGGAGCCAGCGGGTGAAAGCTCGTGAACTCAGTGAGCACAATGGACACA
TCACAGGTATTCACTGGGCTCCCAAGAGCGACCGCATCGTCACTTGCGGGGTAGACCGCAATGCCTATGTCTGGAGTCAG
AAAGATGGTGTCTGGAAGCCAACCCTGGTGATCCTTAGAATTAATCGTGCAGCTACTTTTGTGAAGTGGTTCCCCCTAGA
GAACAAATTTGCTGTGGGAAGTGGAACATGACTCATTTCTGTTTGTTACTTTGAGTCTGAAAATGACTGGTGGGTAAACA
AGCATATTAAAAAGCCGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAACAATGTTTTGCTGGCAGCAGGATCA
TGTGACTTCAAATGCAGAGTGTTTTCTGCTTACATTAAAGAAGTGGATGAAAAGCCAGCCAGCATGCCCTGGGGCACCAA
GATGCCTTTTGGGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCTCTGGTGGCTGGGTCCACGGGGTAAGCTTCTCTGCCA
GTGGGAGCCGCCTGGCCTGGGTCAGCCAGGACAGCACCGTTATCTGTTGCTGATGCCTCAAAAAGTGTGCAGGTCTCAAT
TCTGAAGACAGAGTTCCTACCACTCCTGAGTGTGACATTTGTCTCAGAGAACAGTGTTGTGGCTGCTGGCCATGACTGCT
ACCCAATGCTCTTTAATTATGATGACCGCAGCTGCCTGACCTTCGTCTCCAAGTTAGACATTCCAAAACAGAGCATCCAA
CGCAACATGTCTGCCATAGAACACTTCCGCAACATGGACAAGAGGGCCACGACTGAGGACCACAACATGGCCTTGGAGAG
GCTGCACCAGAATAGCATCACTCAAGTCTCTATTTATGAGGTAGACAAGCAAGGTTGTCGCAAATTTTGCACTACTGGCA
TTGATGGAGCCATGAAAATTTGGGATTTCAAGACCCTCGAGTGTTCCATCCAGGTCCTCCGCATA

Alignment

ORF - retro_ggor_1455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.31 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKAHELKEHNGHITGIDWAPKSDRIVTCG
          SLHQFLLEPITC.AWNRDRT.IALSP.N.E.HIYKK.GSQ.VKA.EL.EHNGHITGI.WAPKSDRIVTCG
Retrocopy SLHQFLLEPITCRAWNRDRTEIALSPDNQEAHIYKKHGSQRVKARELSEHNGHITGIHWAPKSDRIVTCG

Parental  ADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKPI
          .DRNAYVWSQKDGVWKPTLVILRINRAATFVKW.PLENKFAVGSG..LISVCYFESENDWWV.KHIKKPI
Retrocopy VDRNAYVWSQKDGVWKPTLVILRINRAATFVKWFPLENKFAVGSGT*LISVCYFESENDWWVNKHIKKPI

Parental  RSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELM--FESSSSCGWVHGVC
          RSTVLSLDWHPNNVLLAAGSCDFKCR.FSAYIKEV.E.PA..PWG.KMPFG.LM..F..S.S.GWVHGV.
Retrocopy RSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKPASMPWGTKMPFGQLMSEFGGSGSGGWVHGVS

Parental  FSASGSRVAWVSHDSTV-CLSDAEKKMAVATLASETLPLLALTFITDNSLVAAGHDCFPVLFTYDAAAGM
          FSASGSR.AWVS.DSTV....DA.K...V..L..E.LPLL..TF...NS.VAAGHDC.P.LF.YD.....
Retrocopy FSASGSRLAWVSQDSTV>SVADASKSVQVSILKTEFLPLLSVTFVSENSVVAAGHDCYPMLFNYDDRS-C

Parental  LSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGGTAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTT
          L.F...LD.PKQS.QR...A.E.F.N.DK.A..E....A...L..LH.NS..Q.S.....K..C..FCTT
Retrocopy LTFVSKLDIPKQSIQRNMSAIEHFRNMDKRATTEDHNMA---LERLHQNSITQVSIYEVDKQGCRKFCTT

Parental  GMDGGMSIWDVKSLESALKDLKI
          G.DG.M.IWD.K.LE.....L.I
Retrocopy GIDGAMKIWDFKTLECSIQVLRI

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	0.43 RPM	31.41 RPM
SRP007412_cerebellum	0.32 RPM	21.75 RPM
SRP007412_heart	0.19 RPM	26.74 RPM
SRP007412_kidney	0.41 RPM	50.05 RPM
SRP007412_liver	0.21 RPM	46.77 RPM
SRP007412_testis	0.21 RPM	30.46 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_1455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1455 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1340

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046248	2 retrocopies	retro_btau_1547, retro_btau_473,
Canis familiaris	ENSCAFG00000015081	1 retrocopy	retro_cfam_1568,
Callithrix jacchus	ENSCJAG00000015849	1 retrocopy	retro_cjac_2365,
Echinops telfairi	ENSETEG00000009924	2 retrocopies	retro_etel_1076, retro_etel_1275,
Gorilla gorilla	ENSGGOG00000013186	2 retrocopies	retro_ggor_1337, retro_ggor_1455 ,
Microcebus murinus	ENSMICG00000017424	1 retrocopy	retro_mmur_602,
Myotis lucifugus	ENSMLUG00000010933	1 retrocopy	retro_mluc_974,
Mustela putorius furo	ENSMPUG00000016522	1 retrocopy	retro_mputfur_1578,
Mus musculus	ENSMUSG00000029622	2 retrocopies	retro_mmus_1340, retro_mmus_3623,
Otolemur garnettii	ENSOGAG00000010872	2 retrocopies	retro_ogar_2380, retro_ogar_3087,
Rattus norvegicus	ENSRNOG00000000991	2 retrocopies	retro_rnor_1105, retro_rnor_967,
Sus scrofa	ENSSSCG00000007625	1 retrocopy	retro_sscr_374,