RetrogeneDB ID: retro_pabe_2253

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:127463480..127463806(+)
• Located in intron of: ENSPPYG00000014073

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAP18
• Ensembl ID: ENSPPYG00000005198
• Aliases: None
• Description: Histone deacetylase complex subunit SAP18 [Source:UniProtKB/Swiss-Prot;Acc:Q5RDT5]

Sequence

>retro_pabe_2253
AGGCCCGCTGCCGCCAGTAACAGCCGCCGCCACCGAATGGTCGAGTTCTCCCTAGGAAACATACCGTCCAGCGTGCTGGC
GACCTACACTTGGATAGATGCAACCTTGAAAGAACTGAGCTTAGTAAAATAAGTCTATCCAGAGGCTAGAAAGAAGGGCA
CACATTTCAATTTTGCAGTCGTTTTTACAGATATTAAAAGATCTGGCTATCGAGTTAAGGAGATTGGCCAGCACCACGTC
TGGCAGAAAGGGGACTGGTGATTCCATGACTCCTGCAGTCACGGAAGTTACAACTAGGAGATTATTGGGACATAACGATT
ACTCCC

Alignment

ORF - retro_pabe_2253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 71.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVFTTNNGRHHRMDEFSRGNVPSSELQIYTWMDATLKELTSLVKEVYPEARKKGTHFNFAIVFTDVKRPG
          R.....N.R.HRM.EFS.GN.PSS.L..YTW.DATLKEL.SLVK.VYPEARKKGTHFNFA.VFTD.KR.G
Retrocopy RPAAASNSRRHRMVEFSLGNIPSSVLATYTWIDATLKEL-SLVK*VYPEARKKGTHFNFAVVFTDIKRSG

Parental  YRVKEIG-STMSGRKGTDDSMT-LQSQKFQIGDYLDIAITP
          YRVKEIG.ST.SGRKGT.DSMT.LQS.K.Q.GDY.DI.ITP
Retrocopy YRVKEIG>STTSGRKGTGDSMT>LQSRKLQLGDYWDITITP

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	79.12 RPM
SRP007412_cerebellum	0.00 RPM	68.10 RPM
SRP007412_heart	0.00 RPM	44.07 RPM
SRP007412_kidney	0.00 RPM	112.33 RPM
SRP007412_liver	0.00 RPM	197.63 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2253 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2253 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2759
Pan troglodytes	retro_ptro_1866
Callithrix jacchus	retro_cjac_1601

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018631	1 retrocopy	retro_btau_1443,
Canis familiaris	ENSCAFG00000032070	3 retrocopies	retro_cfam_561, retro_cfam_733, retro_cfam_979,
Callithrix jacchus	ENSCJAG00000018645	3 retrocopies	retro_cjac_1601, retro_cjac_2804, retro_cjac_2935,
Cavia porcellus	ENSCPOG00000008598	1 retrocopy	retro_cpor_897,
Dasypus novemcinctus	ENSDNOG00000015204	3 retrocopies	retro_dnov_1027, retro_dnov_119, retro_dnov_1600,
Equus caballus	ENSECAG00000013508	1 retrocopy	retro_ecab_321,
Erinaceus europaeus	ENSEEUG00000006309	1 retrocopy	retro_eeur_674,
Echinops telfairi	ENSETEG00000005565	11 retrocopies	retro_etel_1176, retro_etel_1379, retro_etel_1411, retro_etel_1716, retro_etel_1811, retro_etel_262, retro_etel_456, retro_etel_708, retro_etel_879, retro_etel_891, retro_etel_98,
Felis catus	ENSFCAG00000007026	1 retrocopy	retro_fcat_1450,
Homo sapiens	ENSG00000150459	2 retrocopies	retro_hsap_2186, retro_hsap_2759,
Loxodonta africana	ENSLAFG00000030963	2 retrocopies	retro_lafr_338, retro_lafr_358,
Microcebus murinus	ENSMICG00000004309	2 retrocopies	retro_mmur_1092, retro_mmur_1312,
Myotis lucifugus	ENSMLUG00000002852	4 retrocopies	retro_mluc_1903, retro_mluc_2197, retro_mluc_2239, retro_mluc_407,
Macaca mulatta	ENSMMUG00000010416	2 retrocopies	retro_mmul_465, retro_mmul_914,
Mustela putorius furo	ENSMPUG00000000607	1 retrocopy	retro_mputfur_35,
Mus musculus	ENSMUSG00000021963	1 retrocopy	retro_mmus_82,
Nomascus leucogenys	ENSNLEG00000001995	2 retrocopies	retro_nleu_2922, retro_nleu_315,
Oryctolagus cuniculus	ENSOCUG00000012716	1 retrocopy	retro_ocun_915,
Otolemur garnettii	ENSOGAG00000010062	2 retrocopies	retro_ogar_2213, retro_ogar_650,
Pongo abelii	ENSPPYG00000005198	2 retrocopies	retro_pabe_2066, retro_pabe_2253 ,
Pan troglodytes	ENSPTRG00000005692	2 retrocopies	retro_ptro_1664, retro_ptro_1866,
Rattus norvegicus	ENSRNOG00000010732	1 retrocopy	retro_rnor_163,
Sorex araneus	ENSSARG00000004923	3 retrocopies	retro_sara_232, retro_sara_471, retro_sara_743,
Ictidomys tridecemlineatus	ENSSTOG00000005735	3 retrocopies	retro_itri_1114, retro_itri_1382, retro_itri_1627,
Tursiops truncatus	ENSTTRG00000016912	3 retrocopies	retro_ttru_115, retro_ttru_1453, retro_ttru_381,