RetrogeneDB ID: retro_pabe_3224

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7_random:7818424..7818937(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA8
• Ensembl ID: ENSPPYG00000001526
• Aliases: None
• Description: cell division cycle associated 8 [Source:HGNC Symbol;Acc:14629]

Sequence

>retro_pabe_3224
TCCCCACAGCCTCCACCGAGCATCATGGCTCCTAGGAAGGGCAGCAGTTGGGTAGCCAAGACCAACTCCTTAGGGAGGTG
GAAGCTCACCTCCTTTCTTAAAGACTTTGACCGTGAAGTGGAAATATGAATCAAGCCAACTGAGTCAGTCAGGCAGAACC
TCTTCAAGGAGATGGATAACCTCTACAACATCCAGATCCTGTGGCTCCCCTAGGCGCTGCGCAAAGATGAATGTCTCAAC
TACTTCTCCTTTGGAGGAAACAAACAAGGCTTAGAAGAGGCAGCAAAAGCTGACCTGGATATCACTGAAATAAGCAAACT
AACTGCAGGAGCTATTCAAACACCCCTGAAATCTACTAAAGCATGAAGGATGATACAAGTAGATGAAATGATAGTGGAAG
AGAACGAAGAAGAGGAAAATATACACAGGGATCTTCAAACTGCAAGAGTCAAAAGGTGACCTCCATCCAAGAAGAGAACT
CAGTCTGTACAAGAAAAAGGCAGAAGAGAAAGG

Alignment

ORF - retro_pabe_3224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 52.62 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPQPPPSAMAPRKGSSRVAKTNSLRRRKLASFLKDFDREVEIRVKQIESDRQNLLKEVDNLYNIEILRLP
          SPQPPPS.MAPRKGSS.VAKTNSL.R.KL.SFLKDFDREVEI..K..ES.RQNL.KE.DNLYNI.IL.LP
Retrocopy SPQPPPSIMAPRKGSSWVAKTNSLGRWKLTSFLKDFDREVEI*IKPTESVRQNLFKEMDNLYNIQILWLP

Parental  KALREMNWLDYFALGGNKQALEEAATADLDITEINKLTAEAIQTPLKSAKTRKVIQVDEMIVEEEEEEEN
          .ALR....L.YF..GGNKQ.LEEAA.ADLDITEI.KLTA.AIQTPLKS.K....IQVDEMIVEE.EEEEN
Retrocopy *ALRKDECLNYFSFGGNKQGLEEAAKADLDITEISKLTAGAIQTPLKSTKA*RMIQVDEMIVEENEEEEN

Parental  EHKNLQTARVKRCPPSKKRTQSIQGKGKRKR
          .H..LQTARVKR.PPSKKRTQS.Q.KG.R.R
Retrocopy IHRDLQTARVKR*PPSKKRTQSVQEKGRRER

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	0.06 RPM	0.33 RPM
SRP007412_cerebellum	0.12 RPM	0.36 RPM
SRP007412_heart	0.09 RPM	0.15 RPM
SRP007412_kidney	0.07 RPM	0.27 RPM
SRP007412_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3224 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3224 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,