RetrogeneDB ID: retro_pvam_488

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3435:393674..394094(+)
• Located in intron of: ENSPVAG00000009414

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23
• Ensembl ID: ENSPVAG00000002277
• Aliases: None
• Description: ribosomal protein L23 [Source:HGNC Symbol;Acc:10316]

Sequence

>retro_pvam_488
ATGTCGAAGCGAGGACATGGTGGGTCCTCTGGTGCAAAATTCCGGATTTCTCTGGGCCTTCTGGTAGGAGCCGTCATCAA
CTGTGCTGACAATACAAGAGCCAAAAATGTGTATATTATCTCTGTGAAGGGGATAAAGGGAAGACTGAAAAGACTTCCTG
CTGCTGGTGTGGGTGACATGGTGATGGCCACAGTCAAGAAAGGCAAACCAGAGCTCAGAAAGAAAGTACATCCAGCGGTG
GTAATTCAACAACGAAAGTCATACCGGAGAAAAGGTGGTGTGTTTCTTTATTTTGAAGATAATGCAGGGGTCATAGTAAA
CAATAAAGGCGAAATGAAAGGTTCTGGCATCACAGGACCAGTTGCAAAGGAGTGTGCAGATTTGTGGCCCAGGACTGCAT
CCAATGCTGGCAGCATTGCA

Alignment

ORF - retro_pvam_488 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGKP
          MSKRG.GGSSGAKFRISLGL.VGAVINCADNT.AKN.YIISVKGIKGRL.RLPAAGVGDMVMATVKKGKP
Retrocopy MSKRGHGGSSGAKFRISLGLLVGAVINCADNTRAKNVYIISVKGIKGRLKRLPAAGVGDMVMATVKKGKP

Parental  ELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWPRIASNAGSIA
          ELRKKVHPAVVI.QRKSYRRK.GVFLYFEDNAGVIVNNKGEMKGS.ITGPVAKECADLWPR.ASNAGSIA
Retrocopy ELRKKVHPAVVIQQRKSYRRKGGVFLYFEDNAGVIVNNKGEMKGSGITGPVAKECADLWPRTASNAGSIA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_488 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 92 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004268	6 retrocopies	retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Bos taurus	ENSBTAG00000003229	5 retrocopies	retro_btau_1588, retro_btau_349, retro_btau_65, retro_btau_953, retro_btau_974,
Callithrix jacchus	ENSCJAG00000008311	9 retrocopies	retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Gorilla gorilla	ENSGGOG00000025082	9 retrocopies	retro_ggor_1574, retro_ggor_1744, retro_ggor_1746, retro_ggor_2416, retro_ggor_2508, retro_ggor_256, retro_ggor_2710, retro_ggor_2757, retro_ggor_504,
Latimeria chalumnae	ENSLACG00000004430	1 retrocopy	retro_lcha_16,
Myotis lucifugus	ENSMLUG00000015673	9 retrocopies	retro_mluc_1262, retro_mluc_1523, retro_mluc_1598, retro_mluc_1792, retro_mluc_184, retro_mluc_2051, retro_mluc_2410, retro_mluc_447, retro_mluc_560,
Macaca mulatta	ENSMMUG00000004502	9 retrocopies	retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Nomascus leucogenys	ENSNLEG00000000642	7 retrocopies	retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Oryctolagus cuniculus	ENSOCUG00000013915	6 retrocopies	retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii	ENSOGAG00000012445	7 retrocopies	retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps	ENSOPRG00000001957	10 retrocopies	retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481, retro_opri_639, retro_opri_684,
Pteropus vampyrus	ENSPVAG00000002277	2 retrocopies	retro_pvam_488 , retro_pvam_890,
Rattus norvegicus	ENSRNOG00000004107	10 retrocopies	retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Ictidomys tridecemlineatus	ENSSTOG00000014279	2 retrocopies	retro_itri_122, retro_itri_1577,