RetrogeneDB ID: retro_pabe_477

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:190391191..190391502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC25
• Ensembl ID: ENSPPYG00000018468
• Aliases: None
• Description: Coiled-coil domain-containing protein 25 [Source:UniProtKB/Swiss-Prot;Acc:Q5R9S1]

Sequence

>retro_pabe_477
GGAAAGAGTATAGAAGACATTCCAAAGGAAGTGCTGATGGACTGTGCCCACCTTGTGAAAGCCAGTAGCATTCAAGGCTG
CAAGATGAACGTTAATGTGGTATATACGCCGCGGTCTAACCTGGAGAAAACAGCTGACATGGATGTGGGGCACATAGGTT
TTCACAGGCAGAAGGATGTAAAAATTGTGACAGGGGAGAAGAAAGTAAATGAGATCCTGAACCGATTAGAAAATACCAAA
GTGGAGTGTTTCCAGACCTAGCAGCAGAGAAAGAATGCAGAGATCGTGAAGAGAGGAATGAGAAAAAAGCC

Alignment

ORF - retro_pabe_477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.62 %
• Parental protein coverage: 50.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GENIEDIPKEVLMDCAHLVKANSIQGCKMNNVNVVYTPWSNLKKTADMDVGQIGFHRQKDVKIVTVEKKV
          G..IEDIPKEVLMDCAHLVKA.SIQGCKMN.VNVVYTP.SNL.KTADMDVG.IGFHRQKDVKIVT.EKKV
Retrocopy GKSIEDIPKEVLMDCAHLVKASSIQGCKMN-VNVVYTPRSNLEKTADMDVGHIGFHRQKDVKIVTGEKKV

Parental  NEILNRLEKTKVE-RFPDLAAEKECRDREERNEKKA
          NEILNRLE.TKVE..FPDLAAEKECRDREERNEKKA
Retrocopy NEILNRLENTKVE<VFPDLAAEKECRDREERNEKKA

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	0.11 RPM	24.16 RPM
SRP007412_cerebellum	0.12 RPM	14.35 RPM
SRP007412_heart	0.00 RPM	7.59 RPM
SRP007412_kidney	0.03 RPM	15.58 RPM
SRP007412_liver	0.03 RPM	9.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_477 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_477 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_477 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_141

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012971	2 retrocopies	retro_chof_2254, retro_chof_847,
Dipodomys ordii	ENSDORG00000006595	1 retrocopy	retro_dord_491,
Echinops telfairi	ENSETEG00000006478	1 retrocopy	retro_etel_434,
Homo sapiens	ENSG00000147419	1 retrocopy	retro_hsap_1701,
Gorilla gorilla	ENSGGOG00000009685	1 retrocopy	retro_ggor_1274,
Monodelphis domestica	ENSMODG00000015976	1 retrocopy	retro_mdom_511,
Pongo abelii	ENSPPYG00000018468	2 retrocopies	retro_pabe_1364, retro_pabe_477 ,
Pan troglodytes	ENSPTRG00000020109	1 retrocopy	retro_ptro_141,
Sarcophilus harrisii	ENSSHAG00000018434	1 retrocopy	retro_shar_723,
Tarsius syrichta	ENSTSYG00000000732	1 retrocopy	retro_tsyr_1364,