RetrogeneDB ID: retro_ggor_1337

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:22973257..22974306(-)
• Located in intron of: ENSGGOG00000003620

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_1337
ATGTCACTGCATCAGTTTTTACTAGAGCCAATCAACTGTCGTGCCTGAAACAGGGATCGTACCCAGATTGCCCTCAGTGT
CAATAATCACGAAGTGCACATCTATAAGAAGAATGGGCGCCAGTGTGTGAAAGCTCACGAACTCAAGGAGCACAATGGAC
ACATCACAGATACTGACTGGGCTCCCAAGAGTGACCACATCGTCATTTGTGGGGCAGACCACAATGCCTATGCCTGCAGT
CAGAAAGATGGTGTCTGGAAGCCAACACTGATGATCCTGAGAATTAATCGCACAGCTACTTTTGTGAAGTGGTCCGCCCT
AGAGAACAAATTTGCTGTGGGAAGTGAAGCACGACTCATTTCAGTTTGTTACTTTGAGTCTGAAAATGACTGGTGGGTGA
GCAAGCACATTAAAAAGCTGATTCGCTCCACAGTCCTCAGCTTGGATTGGCATCCCAACAATGTTTTGCTGGCAGCAGGA
TCATGTGACTTCAAACACAGAGTGTTTTCTTCCTACATTAAAGAAGTGGATGAAAAGCTGGCCAGCATGCCCTGGGACAG
CAAGATGCTTTTTGGGCAGCTGATGTCAGAGTTTGGTGGCAGTGGCACTGGTGGCTGGGTCCACGGGGTCAGCTTCTCCG
CCAGTGGGAGCCACCTGGCCTGGGCCAGCCACGACAGCACCATGTCTGCTGCTGATGCCTCAAAAAGTGTGCATGTCTCA
ATCTGAAGACGGAGTTCCAGCTGCTCCTGAGTGTGTCATCTGTCTCAGACAACAGCGCCGTGGCTGCTGGCCATGACTGC
TGACCAATGCTCTTGAACTACGATGACCGTGGCTGCCTGACCTTTGTCTCCAAGTTAGACATTCCAAAACAGAGCATCCA
ACGCAACATGTCTGCCATGGAATGCTTCTGCAACATGGACAAGAGGGCCATGACTGAGGGCTGCAACATGGCTTTGAAGA
TGCTGCACCAGAATAGCATCACTCAAGTCTCTATTTATGAGGTGGACGAGAAAGATTGTCGCAAATATTGCACTACTGGC
ATCAATGGA

Alignment

ORF - retro_ggor_1337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.73 %
• Parental protein coverage: 94.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGSQWVKAHELKEHNGHITGIDWAPKSDRIVTC
          MSLHQFLLEPI.C.A.NRDRTQIALS.NNHEVHIYKKNG.Q.VKAHELKEHNGHIT..DWAPKSD.IV.C
Retrocopy MSLHQFLLEPINCRA*NRDRTQIALSVNNHEVHIYKKNGRQCVKAHELKEHNGHITDTDWAPKSDHIVIC

Parental  GADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLISVCYFESENDWWVSKHIKKP
          GAD.NAY..SQKDGVWKPTL.ILRINR.ATFVKWS.LENKFAVGS.ARLISVCYFESENDWWVSKHIKK.
Retrocopy GADHNAYACSQKDGVWKPTLMILRINRTATFVKWSALENKFAVGSEARLISVCYFESENDWWVSKHIKKL

Parental  IRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELM--FESSSSCGWVHGV
          IRSTVLSLDWHPNNVLLAAGSCDFK.R.FS.YIKEV.E..A..PW.SKM.FG.LM..F..S...GWVHGV
Retrocopy IRSTVLSLDWHPNNVLLAAGSCDFKHRVFSSYIKEVDEKLASMPWDSKMLFGQLMSEFGGSGTGGWVHGV

Parental  CFSASGSRVAWVSHDSTVCLSDAE-KKMAVATLASETLPLLALTFITDNSLVAAGHDCFPVLFTYDAAAG
          .FSASGS..AW.SHDST....DA..KK.A...L..E...LL......DNS.VAAGHDC.P.L..YD...G
Retrocopy SFSASGSHLAWASHDSTMSAADAS<KKCACLNLKTEFQLLLSVSSVSDNSAVAAGHDC*PMLLNYD-DRG

Parental  MLSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGGTAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCT
          .L.F...LD.PKQS.QR...A.E.F.N.DK.A..EG...A...L..LH.NS..Q.S........C...CT
Retrocopy CLTFVSKLDIPKQSIQRNMSAMECFCNMDKRAMTEGCNMA---LKMLHQNSITQVSIYEVDEKDCRKYCT

Parental  TGMDG
          TG..G
Retrocopy TGING

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	0.38 RPM	31.41 RPM
SRP007412_cerebellum	0.32 RPM	21.75 RPM
SRP007412_heart	0.22 RPM	26.74 RPM
SRP007412_kidney	0.16 RPM	50.05 RPM
SRP007412_liver	0.11 RPM	46.77 RPM
SRP007412_testis	0.52 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_1337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1337 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3191
Pan troglodytes	retro_ptro_2253
Pongo abelii	retro_pabe_2647
Macaca mulatta	retro_mmul_2012

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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,