RetrogeneDB ID: retro_pvam_326

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2550:135123..135940(-)
• Located in intron of: ENSPVAG00000016329

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSPVAG00000010380
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_pvam_326
AGAAAACTGTTTCCCAGTGGTTTGAGCTTTGCAACTATAAGTGATAGTTTAAGAGAACATTGTAAAAAAATGGGGCACAC
TCACAGATAGTGTGGTGATGAGAGACCCCCAAACAAAATGTTCCAGGAACTGTGGTTTTTGTAACTTATTTTGTGTAGAA
AAAGGTGGTTGCAGTAATGTGTGCTCGACCATACACAAGATTGATGGGTGTGTAGGGGAACCAAAGAGAGCTGTTTCTAG
AGAGGATTTGGTAAAGCCTGGAGCCCATCTAACAGTGAAGAAAATTTTCGTTGGTGGTATTAAAGAAGATAAAGAAGAAT
ATAATTCGAGAGACTACTTTGAAATGTATGGCAAAAATGAAACTAGAAAAGTTATGGAAGATAGGCAGGGTGGGGAAAGA
AAGATTTGCTTTTGTAAATTTTGATGATCATAATACAATTGATAAAATTGTTTTTCAGAAATACCAAACTATTAATGGGC
ATAACTGTTAAGTGAAAAAAGCCCTTTCTAAACAGGAAATGCAGTCTTTTGGATCGCAAAGAGGTCATGGTGGTGGACCT
GGCAACTTTATGGGTTGCAGAGGAAACTGTAGAGGTGGTGGAGGTAACTTTGGCCATGGTGAAAACTTTGGTGAAAGAGG
AATCTATGGTGGTGAAGATAGTTTGGAGGAGGTGATGGTGGATATAATGGACTTGGAGGTGATGGTGGCAACTATGGCAG
TGGTCTTGGTCATAGTAGTAGAGAAAGCTATGGTAGTGGTGGCGGTGGTGGACCAGGAGGATATGAAAACCAAGGTGTTG
GATATGGTGGTGGTGGT

Alignment

ORF - retro_pvam_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 72.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKLFIGGLSFETTDDSLREH-FEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAA-MCARPHKVDG
          RKLF..GLSF.T..DSLREH...KWGTLTD.VVMRDPQTK.SR..GF....CVE.......C...HK.DG
Retrocopy RKLFPSGLSFATISDSLREH>VKKWGTLTDSVVMRDPQTKCSRNCGFCNLFCVEKGGCSNVCSTIHKIDG

Parental  RVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSG-KKRGFAF
          .V.EPKRAVSRED.VKPGAHLTVKKIFVGGIKED.EEYN.RDYFE.YGK.ET..VMEDRQ.G.K.R.FAF
Retrocopy CVGEPKRAVSREDLVKPGAHLTVKKIFVGGIKEDKEEYNSRDYFEMYGKNETRKVMEDRQGG>KER-FAF

Parental  VTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGGGNFGRGG
          V.FDDH.T.DKIV.QKY.TINGHNC.VKKALSKQEMQS.GSQRG.GGG.GNFMG..GN..GGGGNFG.G.
Retrocopy VNFDDHNTIDKIVFQKYQTINGHNC*VKKALSKQEMQSFGSQRGHGGGPGNFMGCRGNCRGGGGNFGHGE

Parental  NFGGRGGYGGGGGSR-GSYGGGDGGYNGFGGDGGNYGGGPGYSSRGGYGGGGGGGPGGYGNQGGGYGGGG
          NFG.RG.YGG......G..GG..G.....GGDGGNYG.G.G.SSR..YG.GGGGGPGGY.NQG.GYGGGG
Retrocopy NFGERGIYGGEDSLE<GGDGGYNG----LGGDGGNYGSGLGHSSRESYGSGGGGGPGGYENQGVGYGGGG

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_326 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 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013497	12 retrocopies	retro_cfam_1214, retro_cfam_1326, retro_cfam_1388, retro_cfam_1548, retro_cfam_1690, retro_cfam_1816, retro_cfam_265, retro_cfam_272, retro_cfam_400, retro_cfam_625, retro_cfam_65, retro_cfam_836,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Macropus eugenii	ENSMEUG00000013622	6 retrocopies	retro_meug_1264, retro_meug_1760, retro_meug_1913, retro_meug_238, retro_meug_470, retro_meug_56,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000000322	9 retrocopies	retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326 ,
Sus scrofa	ENSSSCG00000015988	6 retrocopies	retro_sscr_1110, retro_sscr_1152, retro_sscr_391, retro_sscr_621, retro_sscr_764, retro_sscr_927,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,