RetrogeneDB ID: retro_pvam_1052

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_2497:164570..165018(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS27A
• Ensembl ID: ENSPVAG00000016471
• Aliases: None
• Description: ribosomal protein S27a [Source:HGNC Symbol;Acc:10417]

Sequence

>retro_pvam_1052
ATGCAAATTTTCGTGAAAACCCTTATAGGGAAGACTATCATTCTCGTGGTTGAAGCTTCAGTTACAACAGAAAATGTAAA
GGCCAAGATCCAGGATAAGGAAGGAATTCCTTCTGATCAGCAGATTGACCTTTGCTGGCAAGCAACTGGAAGATGGGCGT
ACCTTGTCTGACTACAACATTCAAAAGGAGTCCACTCTTCATGTTGCGTTGAGACTTCATGGTGGTGCTAAGATAAGGAA
GAAGTCTTATACCACTCCCAAGAAGAATAAGCAAAAGAGAAAGAAGGTTAAGCTGTCTGTTCTGTAATACTGTAAGGTGG
ATGAGAATGGCAAAATCAGTCGTCTTCACCGGGAGTGCCCTTCAGATGAATGTGGTGATGGAGTTTTTATGGCTAGCCGC
TTTGACAGACATTATTGTGGCAAATGTTGTCTGACCTATTGCTTCAAT

Alignment

ORF - retro_pvam_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQ-RLIFAGKQLEDGRTLSDYNIQKESTLHL
          MQIFVKTL.GKTI.L.VE.S.T.ENVKAKIQDKEGI.P..Q.RL.FAGKQLEDGRTLSDYNIQKESTLH.
Retrocopy MQIFVKTLIGKTIILVVEASVTTENVKAKIQDKEGI-PSDQ>RLTFAGKQLEDGRTLSDYNIQKESTLHV

Parental  VLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMASHFDRH
          .LRL.GGAK.RKK.SYTTPKKNK.KRKKVKL.VL.Y.KVDENGKISRL.RECPSDECG.GVFMAS.FDRH
Retrocopy ALRLHGGAKIRKK-SYTTPKKNKQKRKKVKLSVL*YCKVDENGKISRLHRECPSDECGDGVFMASRFDRH

Parental  YCGKCCLTXXXN
          YCGKCCLT...N
Retrocopy YCGKCCLTYCFN

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_1052 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 16 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004017	5 retrocopies	retro_amel_1565, retro_amel_175, retro_amel_598, retro_amel_661, retro_amel_844,
Canis familiaris	ENSCAFG00000023471	3 retrocopies	retro_cfam_1048, retro_cfam_640, retro_cfam_81,
Callithrix jacchus	ENSCJAG00000010052	5 retrocopies	retro_cjac_200, retro_cjac_229, retro_cjac_344, retro_cjac_74, retro_cjac_88,
Gorilla gorilla	ENSGGOG00000007678	9 retrocopies	retro_ggor_1290, retro_ggor_1291, retro_ggor_1502, retro_ggor_1749, retro_ggor_179, retro_ggor_203, retro_ggor_2373, retro_ggor_2858, retro_ggor_2885,
Loxodonta africana	ENSLAFG00000023133	2 retrocopies	retro_lafr_1122, retro_lafr_185,
Myotis lucifugus	ENSMLUG00000017064	10 retrocopies	retro_mluc_1201, retro_mluc_1255, retro_mluc_1298, retro_mluc_1646, retro_mluc_1730, retro_mluc_1865, retro_mluc_1867, retro_mluc_2264, retro_mluc_37, retro_mluc_380,
Myotis lucifugus	ENSMLUG00000029449	1 retrocopy	retro_mluc_1585,
Macaca mulatta	ENSMMUG00000015563	8 retrocopies	retro_mmul_1198, retro_mmul_193, retro_mmul_2189, retro_mmul_222, retro_mmul_2470, retro_mmul_282, retro_mmul_606, retro_mmul_73,
Monodelphis domestica	ENSMODG00000001819	3 retrocopies	retro_mdom_1367, retro_mdom_1751, retro_mdom_205,
Oryctolagus cuniculus	ENSOCUG00000003613	10 retrocopies	retro_ocun_1087, retro_ocun_1163, retro_ocun_1209, retro_ocun_1259, retro_ocun_1268, retro_ocun_1339, retro_ocun_164, retro_ocun_288, retro_ocun_381, retro_ocun_851,
Pongo abelii	ENSPPYG00000025871	1 retrocopy	retro_pabe_117,
Pan troglodytes	ENSPTRG00000011928	1 retrocopy	retro_ptro_32,
Pteropus vampyrus	ENSPVAG00000016471	3 retrocopies	retro_pvam_1052 , retro_pvam_676, retro_pvam_952,
Rattus norvegicus	ENSRNOG00000004426	2 retrocopies	retro_rnor_117, retro_rnor_161,
Ictidomys tridecemlineatus	ENSSTOG00000009566	5 retrocopies	retro_itri_1583, retro_itri_1765, retro_itri_26, retro_itri_635, retro_itri_962,
Tarsius syrichta	ENSTSYG00000000845	14 retrocopies	retro_tsyr_107, retro_tsyr_122, retro_tsyr_1379, retro_tsyr_1493, retro_tsyr_1520, retro_tsyr_1877, retro_tsyr_1890, retro_tsyr_1892, retro_tsyr_1950, retro_tsyr_2121, retro_tsyr_339, retro_tsyr_767, retro_tsyr_855, retro_tsyr_879,