RetrogeneDB ID: retro_pabe_3649

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:68343537..68343916(+)
• Located in intron of: ENSPPYG00000020441

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC53
• Ensembl ID: ENSPPYG00000004878
• Aliases: None
• Description: coiled-coil domain containing 53 [Source:HGNC Symbol;Acc:24256]

Sequence

>retro_pabe_3649
ATGGATAAAGATGGGCTTCCTCTCATGGGAGTCAGGCGTAGACTTGATCAAGGTGCCAGCTATTCAACAGAAAAGAATGG
TGGCTTTTCTAAACCAAATTGTGGTGCACACTGTATAGTCCCTCAACCGCTCTTCTACATTTAGTGAGGAGAAATTGGCA
AACCTTTATCTTGGTATCCAGCAAATTGAAACAATTCTCAATATTGTAGATGCAAAGTTGCCATCTATACCAGGCCTAGA
TGATGTCACATTTGAAGTATCTCCTTTAAGTGCCACTAGTGTCACAAATGGATCACATTCTGAAGTCATCTCAGAGTAAT
CACAGCAGGACAGTACATAAGACTCTGGACCACAGGAAAGTCAAGTATCAGCAGGAAAT

Alignment

ORF - retro_pabe_3649 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.59 %
• Parental protein coverage: 64.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDEDGLPLMG-SGIDLTKVPAIQQKRTVAFLNQFVVHTVQFLNRFSTVCEEKLADLSLRIQQIETTLNIL
          MD.DGLPLMG.SG.DL.KVPAIQQKR.VAFLNQ.VVHTV..LNR.ST..EEKLA.L.L.IQQIET.LNI.
Retrocopy MDKDGLPLMG>SGVDLIKVPAIQQKRMVAFLNQIVVHTV*SLNRSSTFSEEKLANLYLGIQQIETILNIV

Parental  DAKLSSIPGLDDVTVEVSPLNVTSVTNGAHPEAASEQPQQNSTHDSGLQESEVSAEN
          DAKL.SIPGLDDVT.EVSPL..TSVTNG.H.E..SE..QQ.ST.DSG.QES.VSA.N
Retrocopy DAKLPSIPGLDDVTFEVSPLSATSVTNGSHSEVISE*SQQDST*DSGPQESQVSAGN

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	15.09 RPM
SRP007412_cerebellum	0.00 RPM	22.01 RPM
SRP007412_heart	0.00 RPM	9.84 RPM
SRP007412_kidney	0.00 RPM	19.72 RPM
SRP007412_liver	0.00 RPM	11.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3649 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3649 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3649 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4696
Pan troglodytes	retro_ptro_3121
Gorilla gorilla	retro_ggor_2922
Callithrix jacchus	retro_cjac_4073

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006329	1 retrocopy	retro_amel_791,
Canis familiaris	ENSCAFG00000007270	2 retrocopies	retro_cfam_53, retro_cfam_550,
Callithrix jacchus	ENSCJAG00000014225	1 retrocopy	retro_cjac_4073,
Echinops telfairi	ENSETEG00000002254	1 retrocopy	retro_etel_1917,
Felis catus	ENSFCAG00000019358	1 retrocopy	retro_fcat_498,
Homo sapiens	ENSG00000120860	1 retrocopy	retro_hsap_4696,
Gorilla gorilla	ENSGGOG00000014975	1 retrocopy	retro_ggor_2922,
Loxodonta africana	ENSLAFG00000007850	1 retrocopy	retro_lafr_761,
Macropus eugenii	ENSMEUG00000004888	3 retrocopies	retro_meug_1441, retro_meug_576, retro_meug_629,
Myotis lucifugus	ENSMLUG00000000401	4 retrocopies	retro_mluc_2014, retro_mluc_2015, retro_mluc_2633, retro_mluc_502,
Monodelphis domestica	ENSMODG00000002579	1 retrocopy	retro_mdom_959,
Mus musculus	ENSMUSG00000020056	1 retrocopy	retro_mmus_1773,
Nomascus leucogenys	ENSNLEG00000006365	1 retrocopy	retro_nleu_2366,
Otolemur garnettii	ENSOGAG00000003322	2 retrocopies	retro_ogar_3267, retro_ogar_738,
Pongo abelii	ENSPPYG00000004878	1 retrocopy	retro_pabe_3649 ,
Pan troglodytes	ENSPTRG00000005358	1 retrocopy	retro_ptro_3121,
Ictidomys tridecemlineatus	ENSSTOG00000001870	1 retrocopy	retro_itri_970,
Tupaia belangeri	ENSTBEG00000008498	3 retrocopies	retro_tbel_1036, retro_tbel_1165, retro_tbel_2967,
Tarsius syrichta	ENSTSYG00000000587	4 retrocopies	retro_tsyr_1100, retro_tsyr_265, retro_tsyr_443, retro_tsyr_955,
Tursiops truncatus	ENSTTRG00000017221	4 retrocopies	retro_ttru_1569, retro_ttru_1865, retro_ttru_1919, retro_ttru_935,
Vicugna pacos	ENSVPAG00000002010	1 retrocopy	retro_vpac_446,