RetrogeneDB ID: retro_pabe_2475

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:147853150..147853433(+)
• Located in intron of: ENSPPYG00000015086

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM3
• Ensembl ID: ENSPPYG00000013402
• Aliases: None
• Description: LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17874]

Sequence

>retro_pabe_2475
CAAACTACCAAAACCACAGAGGAAGCCCCTGGATCTTATCAGGCTCAGCCTAGATGAGCAAATTTACATGAAAATGGGAA
ATGACTGATGGCTTCAAGGCAGATTACATGCTTATGATCAACATTTAAATATGATGTTGGGAGATGTAGAAGAAACTGTG
GCTTCTATAGAAATTGATGAATAAACATACGAAGGGATATGTAAATTAATGAAACTGAGTATTCCAATGCTCATTATCCA
GGGAGATGGTGTTGTCCTGGTTGTCCCTCCACTGAAAGTTGGC

Alignment

ORF - retro_pabe_2475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 92.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTTNTVEE-PLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKS
          QTT.T.EE.PLDLIRLSLDE.IY.KM.ND..L.GRLHAYDQHLNM.LGDVEETV..IEIDE.TYE.I.K.
Retrocopy QTTKTTEE>PLDLIRLSLDEQIYMKMGND*WLQGRLHAYDQHLNMMLGDVEETVASIEIDE*TYEGICKL

Parental  TKRNIPMLFVRGDGVVLVAPPLRVG
          .K..IPML...GDGVVLV.PPL.VG
Retrocopy MKLSIPMLIIQGDGVVLVVPPLKVG

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	0.06 RPM	9.51 RPM
SRP007412_cerebellum	0.00 RPM	11.19 RPM
SRP007412_heart	0.00 RPM	11.26 RPM
SRP007412_kidney	0.00 RPM	21.48 RPM
SRP007412_liver	0.00 RPM	12.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2475 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2475 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2986
Pan troglodytes	retro_ptro_2020
Gorilla gorilla	retro_ggor_2068
Macaca mulatta	retro_mmul_1908

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009405	3 retrocopies	retro_amel_1756, retro_amel_659, retro_amel_838,
Bos taurus	ENSBTAG00000007363	1 retrocopy	retro_btau_1732,
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Cavia porcellus	ENSCPOG00000006671	1 retrocopy	retro_cpor_1445,
Dasypus novemcinctus	ENSDNOG00000018032	7 retrocopies	retro_dnov_1046, retro_dnov_135, retro_dnov_1728, retro_dnov_1818, retro_dnov_229, retro_dnov_230, retro_dnov_2408,
Echinops telfairi	ENSETEG00000016207	8 retrocopies	retro_etel_117, retro_etel_1678, retro_etel_1852, retro_etel_2131, retro_etel_472, retro_etel_521, retro_etel_598, retro_etel_833,
Homo sapiens	ENSG00000170860	5 retrocopies	retro_hsap_1045, retro_hsap_1654, retro_hsap_1839, retro_hsap_2286, retro_hsap_2986,
Gorilla gorilla	ENSGGOG00000010006	4 retrocopies	retro_ggor_104, retro_ggor_1699, retro_ggor_2068, retro_ggor_826,
Loxodonta africana	ENSLAFG00000023308	1 retrocopy	retro_lafr_1013,
Myotis lucifugus	ENSMLUG00000010677	4 retrocopies	retro_mluc_1148, retro_mluc_2306, retro_mluc_2337, retro_mluc_25,
Macaca mulatta	ENSMMUG00000023126	5 retrocopies	retro_mmul_1038, retro_mmul_1657, retro_mmul_1908, retro_mmul_554, retro_mmul_828,
Mus musculus	ENSMUSG00000034192	2 retrocopies	retro_mmus_1390, retro_mmus_2446,
Nomascus leucogenys	ENSNLEG00000005079	6 retrocopies	retro_nleu_1138, retro_nleu_2934, retro_nleu_347, retro_nleu_739, retro_nleu_916, retro_nleu_958,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Otolemur garnettii	ENSOGAG00000007659	6 retrocopies	retro_ogar_1031, retro_ogar_231, retro_ogar_242, retro_ogar_2490, retro_ogar_2818, retro_ogar_577,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Pongo abelii	ENSPPYG00000013402	4 retrocopies	retro_pabe_1366, retro_pabe_1936, retro_pabe_2475 , retro_pabe_874,
Pan troglodytes	ENSPTRG00000014650	5 retrocopies	retro_ptro_1125, retro_ptro_1161, retro_ptro_1619, retro_ptro_2020, retro_ptro_712,
Pteropus vampyrus	ENSPVAG00000016795	1 retrocopy	retro_pvam_646,
Rattus norvegicus	ENSRNOG00000008733	1 retrocopy	retro_rnor_1187,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Ictidomys tridecemlineatus	ENSSTOG00000006842	1 retrocopy	retro_itri_613,
Tupaia belangeri	ENSTBEG00000001050	11 retrocopies	retro_tbel_1034, retro_tbel_1343, retro_tbel_2860, retro_tbel_2969, retro_tbel_3184, retro_tbel_331, retro_tbel_3422, retro_tbel_3457, retro_tbel_414, retro_tbel_4663, retro_tbel_794,
Tursiops truncatus	ENSTTRG00000011197	1 retrocopy	retro_ttru_601,