RetrogeneDB ID: retro_ggor_2594

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 7:57041449..57042288(-)
• Located in intron of: ENSGGOG00000009936

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSGGOG00000007719
• Aliases: None
• Description: None

Sequence

>retro_ggor_2594
ATGGCTCCTAGGAAGGGCAGCAGTTGGGTAGCCAAGACCAACTCCTTAGGGAGGTGGAAGCTCGCCTCCTTTCTTAAATA
CTTCGACCATGAAATGGAAATATGAATCAAGCCAATTGAGTCAGTCAGGCAGAACCTCTTCAAGGAGGTGGATAACCTCT
ACAACATCCAGATCCTGTGGCTCCCAAAGGCACTGCGCAAAGATGAATGTCTTAACTACTTCTCCTTTGGAGGCAACAAA
CAAGGCTTAGAAGAGGCAGCAACAGCTGACCTGGATATCACCGAAATAAGCAAACTAACCGCAGAAGCTGTTCAAACACC
CCTGAAATCTACTAAAGCATGAAAGGTGATACAAGTAGATGAAATGATAGTGGAAGAGAATGAAGAAGAGGAAAATAAAC
GCAGGGATCTTCAAACTGCAAGAGTCAAAAGGTGAACTCCATCCAAGAAGAGAACTCAGTCTGTACAAGGAAAAGGCAGA
AGAGAAAGGTCAAGCTGTGCTAACACTGTTACCCAAACTGTGGGCTGATTGGACGTGTCCATAGTGAAACCAACTCCAGG
CCTGATACCCAGGTTTGACTTGAGGGTCTTCATGATCCCTGGCCTGTGCACTCCTGCCACAGGAGAGCGGATTTACAACA
TCTCAGGAAATGGCAGCCCTCTTGCCCATAGCAAAGAGATCTTCCTCACTGTGCCAGCGGGTGGCAAAGAGTGCATGTGA
TTTTTTCCAGTGACTTGCAGAGGCTCAGTATTGCCCAGCTAGATCCGTAGGCCTTGGGAAACATTAAGAAGCTCTCCAAC
CATCTTGCCCAAATCTGCAGCAGCACACACACCCATAAA

Alignment

ORF - retro_ggor_2594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPRKGSSRVAKTNSLRRRKLASFLKDFDREVEIRIKQIESDRQNLLKEVDNLYNIEILRLPKALREMNW
          MAPRKGSS.VAKTNSL.R.KLASFLK.FD.E.EI.IK.IES.RQNL.KEVDNLYNI.IL.LPKALR....
Retrocopy MAPRKGSSWVAKTNSLGRWKLASFLKYFDHEMEI*IKPIESVRQNLFKEVDNLYNIQILWLPKALRKDEC

Parental  LDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVDEMIVEEEEEEENERKNLQTA
          L.YF..GGNKQ.LEEAATADLDITEI.KLTAEA.QTPLKS.K..KVIQVDEMIVEE.EEEEN.R..LQTA
Retrocopy LNYFSFGGNKQGLEEAATADLDITEISKLTAEAVQTPLKSTKA*KVIQVDEMIVEENEEEENKRRDLQTA

Parental  RVRRCPPSKKRTQSIQGKGKRKRSSRANTVTPAVGRLEVSMVKPTPGLTPRFDSRVFKTPGLRTPAAGER
          RV.R..PSKKRTQS.QGKG.R.RSS.ANTVT..VG.L.VS.VKPTPGL.PRFD.RVF..PGL.TPA.GER
Retrocopy RVKR*TPSKKRTQSVQGKGRRERSSCANTVTQTVG*LDVSIVKPTPGLIPRFDLRVFMIPGLCTPATGER

Parental  IYNISGNGSPLADSKEIFLTVPVGGGESL-RLLASDLQRHSIAQLDPEALGNIKKLSNRLAQICSSIRTH
          IYNISGNGSPLA.SKEIFLTVP.GG.E.......SDLQR.SIAQLDP.ALGNIKKLSN.LAQICSS..TH
Retrocopy IYNISGNGSPLAHSKEIFLTVPAGGKECM<VIFSSDLQRLSIAQLDP*ALGNIKKLSNHLAQICSSTHTH

Parental  K
          K
Retrocopy K

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	0.86 RPM
SRP007412_cerebellum	0.00 RPM	0.87 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.65 RPM
SRP007412_liver	0.00 RPM	0.66 RPM
SRP007412_testis	0.00 RPM	46.52 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_2594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2594 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028556	2 retrocopies	retro_acar_139, retro_acar_200,
Choloepus hoffmanni	ENSCHOG00000004959	1 retrocopy	retro_chof_679,
Callithrix jacchus	ENSCJAG00000002008	1 retrocopy	retro_cjac_380,
Homo sapiens	ENSG00000134690	1 retrocopy	retro_hsap_4052,
Gorilla gorilla	ENSGGOG00000007719	2 retrocopies	retro_ggor_2594 , retro_ggor_2721,
Microcebus murinus	ENSMICG00000011926	1 retrocopy	retro_mmur_1589,
Macaca mulatta	ENSMMUG00000014340	2 retrocopies	retro_mmul_1611, retro_mmul_2339,
Nomascus leucogenys	ENSNLEG00000011630	2 retrocopies	retro_nleu_2803, retro_nleu_3006,
Pongo abelii	ENSPPYG00000001526	2 retrocopies	retro_pabe_3224, retro_pabe_3234,
Pan troglodytes	ENSPTRG00000000552	3 retrocopies	retro_ptro_2531, retro_ptro_2533, retro_ptro_2746,