RetrogeneDB ID: retro_ggor_1386

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:58667213..58667573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC59
• Ensembl ID: ENSGGOG00000025296
• Aliases: None
• Description: None

Sequence

>retro_ggor_1386
AAAGTTGTCCAGCCTTTGCTAGAGAACAATGCAGTATTACCTAAGGTTTGTCTGAAGAACACTTCACCATTGAGCAGCTT
CAGCCAGAAGAGCAATGTAGCAAAATGGGTAAACTCCATTACCATTCAAAAAACAAAAAATGAAAGAAACATCAAGTCGC
AAAGCACGAGCAGAATGTGAATAAGTAGAAGCTAAGCATGCTGCTAAGAAACAAGAACGTGAGAGGATAAAATAAGAGAA
AAGCTCAAAGGCTCCTAAGCAAAGAAAATGCAAGTGTTCCAAATATTGAGCAAAAAGACAAGAAAGGGCCAACCAAACTT
GAACTTATACATGGAGTAACTTCTTCATTAAATACATAAA

Alignment

ORF - retro_ggor_1386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.38 %
• Parental protein coverage: 50.62 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QVHQPLLE-EQCSIDQPLFEDQCSFDQPQPEEQSIKT-VNSFTIPKKNK-KKTSNQKAQEEYEQVQAKRA
          .V.QPLLE.EQCSI...L.E......Q.QPEEQ..K..VNS.TI......K.TS..KA..E.E.V.AK.A
Retrocopy KVVQPLLE<EQCSIT*GLSEEHFTIEQLQPEEQCSKM>VNSITIXXXXX>KETSSRKARAECE*VEAKHA

Parental  AKKQEFERRKQEREEAQRQYKK-KKMEVFKILNKKTKKGQPNLNVQMEYLLQKIQE
          AKKQE..R.....E......K..KKM.VF.IL.KKT.KGQPNLN..ME.LL..I..
Retrocopy AKKQE--RERIK*EKSSKAPKQ<KKMQVFQILSKKTRKGQPNLNLYME*LLH*IHK

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	4.75 RPM
SRP007412_cerebellum	0.00 RPM	4.37 RPM
SRP007412_heart	0.00 RPM	1.91 RPM
SRP007412_kidney	0.00 RPM	6.62 RPM
SRP007412_liver	0.00 RPM	5.64 RPM
SRP007412_testis	0.00 RPM	25.80 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_1386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1386 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016875	1 retrocopy	retro_amel_954,
Bos taurus	ENSBTAG00000036282	4 retrocopies	retro_btau_725, retro_btau_726, retro_btau_727, retro_btau_728,
Choloepus hoffmanni	ENSCHOG00000007788	1 retrocopy	retro_chof_1648,
Dasypus novemcinctus	ENSDNOG00000011546	1 retrocopy	retro_dnov_1033,
Dipodomys ordii	ENSDORG00000003005	1 retrocopy	retro_dord_485,
Echinops telfairi	ENSETEG00000000256	2 retrocopies	retro_etel_1338, retro_etel_1789,
Gorilla gorilla	ENSGGOG00000025296	2 retrocopies	retro_ggor_1386 , retro_ggor_99,
Microcebus murinus	ENSMICG00000000967	4 retrocopies	retro_mmur_1456, retro_mmur_354, retro_mmur_689, retro_mmur_909,
Oryctolagus cuniculus	ENSOCUG00000017824	2 retrocopies	retro_ocun_1782, retro_ocun_498,
Otolemur garnettii	ENSOGAG00000004383	1 retrocopy	retro_ogar_2065,
Pan troglodytes	ENSPTRG00000005266	1 retrocopy	retro_ptro_1270,
Tupaia belangeri	ENSTBEG00000008887	7 retrocopies	retro_tbel_1515, retro_tbel_2047, retro_tbel_2126, retro_tbel_302, retro_tbel_3391, retro_tbel_3721, retro_tbel_972,