RetrogeneDB ID: retro_pabe_2772

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:120335297..120335554(-)
• Located in intron of: ENSPPYG00000015708

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR3
• Ensembl ID: ENSPPYG00000014955
• Aliases: None
• Description: ragulator complex protein LAMTOR3 [Source:RefSeq peptide;Acc:NP_001127674]

Sequence

>retro_pabe_2772
AATGATAATGCTCCAGAGCACACTTTGAGATCTAGTTTCTTATCTACTTTTGCCCTTGCACAGATGAAAGGAGAAAACTT
GGACTTTCAAAAAATATAAGTATCATTTGTTACTATAACACCTACCAAGTAGTTCAATTTAATCATTTACCTTTGGTGGT
GAGTTTCATAGCCAGCAGCAATGCCAATATAGGACTAACTGTCAACCCAGAAAAGGGACTTGCTCCATTATTTGAACAAC
TGAGACAAATTGTGGAA

Alignment

ORF - retro_pabe_2772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.46 %
• Parental protein coverage: 69.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NDNAPEHALRPGFLSTFALA-TDQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVS
          NDNAPEH.LR..FLSTFALA.TD...KLGLSKN.SIICYYNTYQVVQFN.LPLVVSFIASS.AN.GL.V.
Retrocopy NDNAPEHTLRSSFLSTFALA<TDERRKLGLSKNISIICYYNTYQVVQFNHLPLVVSFIASSNANIGLTVN

Parental  LEKELAPLFEELRQVVE
          .EK.LAPLFE.LRQ.VE
Retrocopy PEKGLAPLFEQLRQIVE

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	10.28 RPM
SRP007412_cerebellum	0.00 RPM	9.85 RPM
SRP007412_heart	0.03 RPM	5.30 RPM
SRP007412_kidney	0.00 RPM	8.49 RPM
SRP007412_liver	0.00 RPM	5.29 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2772 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2772 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3374
Pan troglodytes	retro_ptro_2294
Gorilla gorilla	retro_ggor_2283
Macaca mulatta	retro_mmul_2104
Callithrix jacchus	retro_cjac_1821

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000995	4 retrocopies	retro_amel_1266, retro_amel_1278, retro_amel_1833, retro_amel_610,
Bos taurus	ENSBTAG00000007923	1 retrocopy	retro_btau_578,
Canis familiaris	ENSCAFG00000029975	3 retrocopies	retro_cfam_1425, retro_cfam_692, retro_cfam_700,
Choloepus hoffmanni	ENSCHOG00000013153	7 retrocopies	retro_chof_1167, retro_chof_1236, retro_chof_1266, retro_chof_1536, retro_chof_166, retro_chof_1929, retro_chof_955,
Callithrix jacchus	ENSCJAG00000015196	4 retrocopies	retro_cjac_1149, retro_cjac_1821, retro_cjac_2581, retro_cjac_2786,
Cavia porcellus	ENSCPOG00000013304	2 retrocopies	retro_cpor_112, retro_cpor_208,
Dasypus novemcinctus	ENSDNOG00000025421	14 retrocopies	retro_dnov_1057, retro_dnov_118, retro_dnov_1190, retro_dnov_1332, retro_dnov_137, retro_dnov_2003, retro_dnov_2213, retro_dnov_2597, retro_dnov_2665, retro_dnov_487, retro_dnov_522, retro_dnov_626, retro_dnov_938, retro_dnov_939,
Dipodomys ordii	ENSDORG00000015501	5 retrocopies	retro_dord_328, retro_dord_379, retro_dord_546, retro_dord_756, retro_dord_771,
Equus caballus	ENSECAG00000013569	1 retrocopy	retro_ecab_138,
Echinops telfairi	ENSETEG00000009065	6 retrocopies	retro_etel_1271, retro_etel_1421, retro_etel_1621, retro_etel_1639, retro_etel_471, retro_etel_794,
Homo sapiens	ENSG00000109270	2 retrocopies	retro_hsap_1190, retro_hsap_3374,
Gorilla gorilla	ENSGGOG00000001132	2 retrocopies	retro_ggor_2283, retro_ggor_928,
Loxodonta africana	ENSLAFG00000015740	1 retrocopy	retro_lafr_480,
Myotis lucifugus	ENSMLUG00000006786	2 retrocopies	retro_mluc_2415, retro_mluc_445,
Macaca mulatta	ENSMMUG00000006830	1 retrocopy	retro_mmul_2104,
Monodelphis domestica	ENSMODG00000020688	3 retrocopies	retro_mdom_1133, retro_mdom_455, retro_mdom_907,
Mustela putorius furo	ENSMPUG00000009569	2 retrocopies	retro_mputfur_590, retro_mputfur_877,
Mus musculus	ENSMUSG00000091512	1 retrocopy	retro_mmus_167,
Nomascus leucogenys	ENSNLEG00000013684	2 retrocopies	retro_nleu_1936, retro_nleu_965,
Otolemur garnettii	ENSOGAG00000005336	4 retrocopies	retro_ogar_2081, retro_ogar_2120, retro_ogar_3435, retro_ogar_451,
Pongo abelii	ENSPPYG00000014955	3 retrocopies	retro_pabe_1268, retro_pabe_2772 , retro_pabe_991,
Pan troglodytes	ENSPTRG00000016310	1 retrocopy	retro_ptro_2294,
Pteropus vampyrus	ENSPVAG00000017674	1 retrocopy	retro_pvam_1378,
Rattus norvegicus	ENSRNOG00000010552	1 retrocopy	retro_rnor_2341,
Sus scrofa	ENSSSCG00000009176	1 retrocopy	retro_sscr_148,
Tupaia belangeri	ENSTBEG00000003682	6 retrocopies	retro_tbel_1932, retro_tbel_2172, retro_tbel_230, retro_tbel_3358, retro_tbel_4521, retro_tbel_924,
Tursiops truncatus	ENSTTRG00000015015	1 retrocopy	retro_ttru_809,