RetrogeneDB ID: retro_pvam_117

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1476:88641..88903(+)
• Located in intron of: ENSPVAG00000003849

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS20
• Ensembl ID: ENSPVAG00000016402
• Aliases: None
• Description: ribosomal protein S20 [Source:HGNC Symbol;Acc:10405]

Sequence

>retro_pvam_117
ATGGCTTTTAAGATACTGGAGAGACACCCATGGAACCTGAGGTGGCAAGTCACTGAATCAGAATTACTCTAACCAGCCGC
AACGTAAAATATTTGGAGAAGGTGTGTGCTGACTTGATCAGAGGTGCAAGGAAAATATCAAAGAGAAAAGACCAGTTCAG
ATGCCTACCAAGACTCTGAGAATCACTGTAAGAAAAACTCTCTGTGGAGAAGGGTCTAAGACTTGGAATCATTTTCACAT
GAGGATCCACAACCGATTCATT

Alignment

ORF - retro_pvam_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 74.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAFK-DTGKTPVEPEVAIHRIRITLTSRNVKSLEKVCADLIRGAKDKNLKVKGPVR-MPTKTLRITTRKT
          MAFK.DTG.TP.EPEVA.H.IRITLTSRNVK.LEKVCADLIRGA..K..K.K...R.MPTKTLRIT.RKT
Retrocopy MAFK<DTGETPMEPEVASH*IRITLTSRNVKYLEKVCADLIRGAR-KISKRKDQFR<MPTKTLRITVRKT

Parental  PCGEGSKTWDRFQMRIHKRLI
          .CGEGSKTW..F.MRIH.R.I
Retrocopy LCGEGSKTWNHFHMRIHNRFI

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_117 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 9 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006087	17 retrocopies	retro_amel_1067, retro_amel_1142, retro_amel_1146, retro_amel_1245, retro_amel_1405, retro_amel_1409, retro_amel_1442, retro_amel_1579, retro_amel_1619, retro_amel_1825, retro_amel_281, retro_amel_299, retro_amel_437, retro_amel_495, retro_amel_599, retro_amel_709, retro_amel_98,
Macropus eugenii	ENSMEUG00000014171	21 retrocopies	retro_meug_100, retro_meug_1015, retro_meug_1058, retro_meug_1170, retro_meug_1313, retro_meug_1614, retro_meug_1702, retro_meug_1761, retro_meug_1777, retro_meug_1831, retro_meug_1911, retro_meug_1951, retro_meug_2065, retro_meug_2110, retro_meug_2187, retro_meug_659, retro_meug_710, retro_meug_723, retro_meug_818, retro_meug_892, retro_meug_928,
Myotis lucifugus	ENSMLUG00000029059	2 retrocopies	retro_mluc_1187, retro_mluc_546,
Macaca mulatta	ENSMMUG00000021314	1 retrocopy	retro_mmul_16,
Monodelphis domestica	ENSMODG00000009114	6 retrocopies	retro_mdom_1701, retro_mdom_1735, retro_mdom_1738, retro_mdom_1814, retro_mdom_1817, retro_mdom_1943,
Mustela putorius furo	ENSMPUG00000010452	15 retrocopies	retro_mputfur_1094, retro_mputfur_1188, retro_mputfur_1313, retro_mputfur_1366, retro_mputfur_1374, retro_mputfur_1432, retro_mputfur_238, retro_mputfur_249, retro_mputfur_320, retro_mputfur_418, retro_mputfur_424, retro_mputfur_433, retro_mputfur_620, retro_mputfur_77, retro_mputfur_819,
Nomascus leucogenys	ENSNLEG00000001214	19 retrocopies	retro_nleu_1013, retro_nleu_1343, retro_nleu_1447, retro_nleu_1566, retro_nleu_1794, retro_nleu_1798, retro_nleu_1805, retro_nleu_1818, retro_nleu_2059, retro_nleu_2159, retro_nleu_2654, retro_nleu_2659, retro_nleu_2750, retro_nleu_2786, retro_nleu_2819, retro_nleu_2843, retro_nleu_3066, retro_nleu_382, retro_nleu_41,
Pteropus vampyrus	ENSPVAG00000016402	8 retrocopies	retro_pvam_117 , retro_pvam_1355, retro_pvam_1358, retro_pvam_554, retro_pvam_638, retro_pvam_660, retro_pvam_77, retro_pvam_800,
Sarcophilus harrisii	ENSSHAG00000011200	10 retrocopies	retro_shar_135, retro_shar_228, retro_shar_418, retro_shar_436, retro_shar_441, retro_shar_443, retro_shar_450, retro_shar_504, retro_shar_544, retro_shar_785,