RetrogeneDB ID: retro_pabe_3449

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:120621411..120621607(+)
• Located in intron of: ENSPPYG00000019592

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSPPYG00000017661
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm5 [Source:RefSeq peptide;Acc:NP_001126628]

Sequence

>retro_pabe_3449
ATGGCGGCTAAGGCTACCACCTACTTGCCCAGCTGTTGCTGCTAGAGCTTGTAGACAAATGTATAGGCTCAAGAATTCGC
ATTGTGGTGAAGAGTAATTAAGAAATTGTGGGTACTCTTCTAGGAGTTGATGACTTTGTCAATACGGACTAGAAGAGGTC
ACTGAGTTTGAAATCACACCAGAAGGAAGAAGTATT

Alignment

ORF - retro_pabe_3449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 72.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAANATTNP-SQLLPLELVDKCIGSRIHIVMKSDKEIVGTLLGFDDFVN-ILLKDVTEFEITPEGRRI
          MAA.ATT....QLL.LELVDKCIGSRI.IV.KS..EIVGTLLG.DDFVN...L..VTEFEITPEGR.I
Retrocopy MAAKATTYL<AQLLLLELVDKCIGSRIRIVVKSN*EIVGTLLGVDDFVN<YGLEEVTEFEITPEGRSI

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	3.15 RPM
SRP007412_cerebellum	0.00 RPM	7.54 RPM
SRP007412_heart	0.00 RPM	3.94 RPM
SRP007412_kidney	0.00 RPM	5.73 RPM
SRP007412_liver	0.00 RPM	3.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3449 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3449 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4216
Pan troglodytes	retro_ptro_2862
Gorilla gorilla	retro_ggor_2824

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 80 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006700	1 retrocopy	retro_amel_453,
Bos taurus	ENSBTAG00000002332	3 retrocopies	retro_btau_1012, retro_btau_1123, retro_btau_1313,
Choloepus hoffmanni	ENSCHOG00000005335	1 retrocopy	retro_chof_1042,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Cavia porcellus	ENSCPOG00000010421	1 retrocopy	retro_cpor_607,
Dasypus novemcinctus	ENSDNOG00000008121	1 retrocopy	retro_dnov_1836,
Equus caballus	ENSECAG00000018445	1 retrocopy	retro_ecab_809,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Homo sapiens	ENSG00000106355	2 retrocopies	retro_hsap_3703, retro_hsap_4216,
Gorilla gorilla	ENSGGOG00000010325	2 retrocopies	retro_ggor_2504, retro_ggor_2824,
Loxodonta africana	ENSLAFG00000029579	3 retrocopies	retro_lafr_1000, retro_lafr_368, retro_lafr_922,
Microcebus murinus	ENSMICG00000005353	3 retrocopies	retro_mmur_1345, retro_mmur_69, retro_mmur_950,
Myotis lucifugus	ENSMLUG00000017028	1 retrocopy	retro_mluc_2439,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Oryctolagus cuniculus	ENSOCUG00000029043	5 retrocopies	retro_ocun_1284, retro_ocun_1452, retro_ocun_1513, retro_ocun_1556, retro_ocun_903,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Ochotona princeps	ENSOPRG00000002443	3 retrocopies	retro_opri_26, retro_opri_562, retro_opri_701,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449 ,
Pan troglodytes	ENSPTRG00000019057	1 retrocopy	retro_ptro_2862,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Sus scrofa	ENSSSCG00000026064	1 retrocopy	retro_sscr_385,
Ictidomys tridecemlineatus	ENSSTOG00000012662	4 retrocopies	retro_itri_1199, retro_itri_188, retro_itri_222, retro_itri_415,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tarsius syrichta	ENSTSYG00000006449	9 retrocopies	retro_tsyr_1022, retro_tsyr_1080, retro_tsyr_1579, retro_tsyr_181, retro_tsyr_1837, retro_tsyr_1863, retro_tsyr_1963, retro_tsyr_577, retro_tsyr_96,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,