RetrogeneDB ID: retro_pvam_1077

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_26876:674..1281(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000009423
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1077
GAGAATTCCCAGTTGTGTAAGCTGTTCATCGGCGGCCTCAATGTGCAGACGAGTGAGTCGGGCCTGCGCGGCCACTTCGA
GGCCTTTGGGACTCTGACGGACTGCGTGGTGGTGGTGAATCCTCAGACCAAGCGCTCCCGTTGCTTTGGCTTCGTGACCT
ACTCCAATGTGGAGGAGGCCGATGCCGCCATGGCCGCCTCGCCCCATGCCGTGGACGGCAACACGGTGGAGCTGAAGCGG
GCGGTGTCCCGGGAGGATTCGGCGCGGCCCGGTGCCCACGCGAAGGTTAAGAAGCTCTTTGTCGGGGGCCTTAACGGAGA
CGTGGACCGAGGGCGACCTGATCGAGCACTTCTCGCAGTTTGGCACCGTGGAAAAGGCCGAGATTATTGCCGACAAGCAG
TCCGGCAAGAAGCGTGGCTTCGGCTTCGTGTATTTTCAGAATCACGACGCGGCAGACAAGGCCGCGGTGGTCAAGTTCCA
TCCGATCCAGGGCCATCGCGTGGAAGTGAAGAAGGCCGTACCCAAGGAGGATATCCACTCCGGTGGGGGTGGAGGCGGCT
CCCGGTCCTCCCGGGGCGGCCGAGGCGGCCGCGGGCGCGGCGGTGGT

Alignment

ORF - retro_pvam_1077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.25 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVDAAMCARPHK
          E..QL.KLFIGGL...T....LR.HFE..GTLTDCVV...PQTKRSR.FGFVTYS.VEE.DAAM.A.PH.
Retrocopy ENSQLCKLFIGGLNVQTSESGLRGHFEAFGTLTDCVVVVNPQTKRSRCFGFVTYSNVEEADAAMAASPHA

Parental  VDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTE-EYNLRDYFEKYGKIETIEVMEDRQSGKKRG
          VDG..VE.KRAVSREDS..PGAH..VKK.FVGG...D...E..L...F...G..E..E...D.QSGKKRG
Retrocopy VDGNTVELKRAVSREDSARPGAHAKVKKLFVGGLNGDVD>EGDLIEHFSQFGTVEKAEIIADKQSGKKRG

Parental  FAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGNFMGRGGNFGGGG
          F.FV.F..HD..DK..V.K.H.I.GH..EVKKA..K....S.G...G.GG......GRGG...GGG
Retrocopy FGFVYFQNHDAADKAAVVKFHPIQGHRVEVKKAVPKEDIHSGG---GGGGSRSSRGGRGGRGRGGG

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_1077 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,