RetrogeneDB ID: retro_ptro_141

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:39999365..39999683(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC25
• Ensembl ID: ENSPTRG00000020109
• Aliases: None
• Description: None

Sequence

>retro_ptro_141
GGAGAGAACATAGAAGACATTCCAAAGGAAGTGCTGATGGACTGTGCCCACCTTGTGAAAGCCAGTAGCATTCAAGGCTG
CAAGATGAACGTTAATGTGGTATATACGCCGCAGTCTAACCTGAAGAAAACAGCTGACATGGATGTGGGGCACATAGGTT
TTCACAGGCAGAAGGATGTAAAAGTTGTGACATGGGAGAAAAAAGTAAATGAGATCCTGAACCGATTAGAAAAGACCAAA
GTGGAGCGGTTCCCAGACCTAGCAGCAGAGAAAGAATGCAGAGATCGTGAAGAGAGGAATGAGAAAACAGCCCAAATT

Alignment

ORF - retro_ptro_141 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GENIEDIPKEVLMDCAHLVKANSIQGCKMNNVNVVYTPWSNLKKTADMDVGQIGFHRQKDVKIVTVEKKV
          GENIEDIPKEVLMDCAHLVKA.SIQGCKMN.VNVVYTP.SNLKKTADMDVG.IGFHRQKDVK.VT.EKKV
Retrocopy GENIEDIPKEVLMDCAHLVKASSIQGCKMN-VNVVYTPQSNLKKTADMDVGHIGFHRQKDVKVVTWEKKV

Parental  NEILNRLEKTKVERFPDLAAEKECRDREERNEKKAQI
          NEILNRLEKTKVERFPDLAAEKECRDREERNEK.AQI
Retrocopy NEILNRLEKTKVERFPDLAAEKECRDREERNEKTAQI

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	0.02 RPM	37.93 RPM
SRP007412_cerebellum	0.00 RPM	30.08 RPM
SRP007412_heart	0.00 RPM	37.10 RPM
SRP007412_kidney	0.00 RPM	32.06 RPM
SRP007412_liver	0.00 RPM	32.67 RPM
SRP007412_testis	0.21 RPM	44.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_141 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_141 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_477

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 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 ,
Tarsius syrichta	ENSTSYG00000000732	1 retrocopy	retro_tsyr_1364,