RetrogeneDB ID: retro_pvam_239

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2066:208682..209048(-)
• Located in intron of: ENSPVAG00000004426

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL12
• Ensembl ID: ENSPVAG00000000925
• Aliases: None
• Description: ribosomal protein L12 [Source:HGNC Symbol;Acc:10302]

Sequence

>retro_pvam_239
CCTAAGTTCCGCCCAAAAGAGATCAAAGTCATATATCTAAAGTGCAAGAACAGGAATTTGGTGCCGTGTCTGCCCTGGCC
CCCAAGATTAGACTGCTGGGTCTTTTTCCAAAAAAGTTTGGTGATGACGTCCAAAGGCAACAAGTGCCTGGAAGGGTCTG
AGGAGTACATGAAACTGATCACTCAGAACAGAGAGGCCCAGGAGGAGTGGTGCCTTCTGCCCCTGCCCTACTGTCAAAGT
CCTCCAGGAACCAGCCAGAGATAGAGAGAAGGAAAAGCTCATCAAGCACCGTGGTAACAGCGGCTTGATGAGATTGTCGA
CACTGCTTGATGGATGCAGCACCGATCTGTATAGCCAGAGAGCTCT

Alignment

ORF - retro_pvam_239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  PKFDPNEVKVVYLRCTGG-EVGATSALAPKIGPLGLSPKKVGDDI-AKATGDWKGLRIT-VKLTIQNRQA
          PKF.P.E.KV.YL.C....E.GA.SALAPKI..LGL.PKK.GDD...KAT..WKGLR.T..KL..QNR.A
Retrocopy PKFRPKEIKVIYLKCKNR<EFGAVSALAPKIRLLGLFPKKFGDDV<PKATSAWKGLRST<MKLITQNREA

Parental  QIE-VVPSASALI-IKALKEPPRDRKKQKNIKHSGNI-TFDEIVNIARQMRHRSLARELS
          Q.E.VVPSA.AL...K.L.EP.RDR.K.K.IKH.GN....DEIV..A..M.HRS...E.S
Retrocopy QEE<VVPSAPALL<VKVLQEPARDREKEKLIKHRGNS<RLDEIVDTA*WMQHRSV*PESS

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_239 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 13 parental genes, and 143 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006963	3 retrocopies	retro_btau_102, retro_btau_2, retro_btau_5,
Callithrix jacchus	ENSCJAG00000018082	1 retrocopy	retro_cjac_221,
Gorilla gorilla	ENSGGOG00000000648	34 retrocopies	retro_ggor_1024, retro_ggor_1059, retro_ggor_1086, retro_ggor_1207, retro_ggor_1242, retro_ggor_1377, retro_ggor_1389, retro_ggor_1449, retro_ggor_1511, retro_ggor_1516, retro_ggor_1530, retro_ggor_1645, retro_ggor_1740, retro_ggor_1753, retro_ggor_1806, retro_ggor_1845, retro_ggor_2158, retro_ggor_221, retro_ggor_2232, retro_ggor_2293, retro_ggor_2304, retro_ggor_232, retro_ggor_2334, retro_ggor_2394, retro_ggor_2414, retro_ggor_2506, retro_ggor_262, retro_ggor_2758, retro_ggor_2768, retro_ggor_2949, retro_ggor_541, retro_ggor_600, retro_ggor_637, retro_ggor_942,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Macaca mulatta	ENSMMUG00000000422	2 retrocopies	retro_mmul_1823, retro_mmul_53,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Mus musculus	ENSMUSG00000038900	1 retrocopy	retro_mmus_28,
Pongo abelii	ENSPPYG00000019622	44 retrocopies	retro_pabe_1009, retro_pabe_1084, retro_pabe_1095, retro_pabe_1127, retro_pabe_1159, retro_pabe_1223, retro_pabe_1246, retro_pabe_1309, retro_pabe_1361, retro_pabe_1471, retro_pabe_1509, retro_pabe_1577, retro_pabe_1659, retro_pabe_1660, retro_pabe_1736, retro_pabe_1794, retro_pabe_1806, retro_pabe_1820, retro_pabe_1969, retro_pabe_1982, retro_pabe_2000, retro_pabe_2149, retro_pabe_2328, retro_pabe_2531, retro_pabe_2802, retro_pabe_2859, retro_pabe_2928, retro_pabe_2947, retro_pabe_3002, retro_pabe_3146, retro_pabe_3185, retro_pabe_3276, retro_pabe_3363, retro_pabe_3405, retro_pabe_3482, retro_pabe_3693, retro_pabe_488, retro_pabe_521, retro_pabe_604, retro_pabe_620, retro_pabe_757, retro_pabe_815, retro_pabe_831, retro_pabe_904,
Pan troglodytes	ENSPTRG00000022808	1 retrocopy	retro_ptro_21,
Pteropus vampyrus	ENSPVAG00000000925	15 retrocopies	retro_pvam_100, retro_pvam_1026, retro_pvam_1193, retro_pvam_209, retro_pvam_239 , retro_pvam_483, retro_pvam_572, retro_pvam_590, retro_pvam_617, retro_pvam_630, retro_pvam_687, retro_pvam_747, retro_pvam_787, retro_pvam_846, retro_pvam_888,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sus scrofa	ENSSSCG00000005612	14 retrocopies	retro_sscr_1111, retro_sscr_127, retro_sscr_189, retro_sscr_28, retro_sscr_439, retro_sscr_526, retro_sscr_551, retro_sscr_71, retro_sscr_715, retro_sscr_772, retro_sscr_773, retro_sscr_828, retro_sscr_832, retro_sscr_911,