RetrogeneDB ID: retro_pabe_1364

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:59800891..59801230(+)
• 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_1364
CATGAAGATCTGATCAAGCACAGCTGGCCTGAAGATATCTGGTTTCGTGCGGACAGACTCTCTTCGGCTCATGTATACCT
TCAACTGCATAAGGAAAAGAATATAGAAGACATTCCAAAGGAAGTGCTGACAGACTGCACCCACCTTGTGAAGGCCAATA
GCATTCAAGGCTGCAAGAACAACGTTAATGTAGTAAATACGCCATGGTCTGACCTGAAGAAAACAGCTGACGTGGATGTG
AGCCAGATAGGCTTTCACAGGCAGAAGGATGTAAAAATTGTGACAATGGAGAAGAAAGTAAATGAGATCCTGAACCGATT
AGAAAAAACCAAAGTGGAA

Alignment

ORF - retro_pabe_1364 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.96 %
• Parental protein coverage: 54.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NEDLIKHGWPEDIWFHVDKLSSAHVYLRLHKGENIEDIPKEVLMDCAHLVKANSIQGCKMNNVNVVYTPW
          .EDLIKH.WPEDIWF..D.LSSAHVYL.LHK..NIEDIPKEVL.DC.HLVKANSIQGCK.NNVNVV.TPW
Retrocopy HEDLIKHSWPEDIWFRADRLSSAHVYLQLHKEKNIEDIPKEVLTDCTHLVKANSIQGCK-NNVNVVNTPW

Parental  SNLKKTADMDVGQIGFHRQKDVKIVTVEKKVNEILNRLEKTKVE
          S.LKKTAD.DV.QIGFHRQKDVKIVT.EKKVNEILNRLEKTKVE
Retrocopy SDLKKTADVDVSQIGFHRQKDVKIVTMEKKVNEILNRLEKTKVE

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	24.16 RPM
SRP007412_cerebellum	0.00 RPM	14.35 RPM
SRP007412_heart	0.00 RPM	7.59 RPM
SRP007412_kidney	0.00 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_1364 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1364 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1364 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1701
Gorilla gorilla	retro_ggor_1274

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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,