RetrogeneDB ID: retro_ogar_3215

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873742.1:1599814..1600479(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSOGAG00000028132
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_ogar_3215
AAGTCAGAGTCTCCTAAAGAGCCCGAACAGCTGCGGAAACTCTTCATTGAAGGGTTGAGCTTTGAAAAGACTGATAAAGA
GTCTGAGGAGCCATTTTGAGCAATGGGGAACGCTTACAGACTGCGAGGTAATGAGAGATCCAAACACCAAGCGCTCCAGG
GGCTTTGGGTTTGTCACCAACGCGGCCCTGGAGGAGGTAGATGCAGCAATGAATGCAAGGCCACACAAGATGGATGGAAG
AGTTGTGGAACCAAAGAGAGCTGTTTCCAGAGAAGATTCTTAAAGACCTGGTGCCCATTTACCTGTGTAAAAGATCTTTG
TTGGTGGCATTGAAGAAGATATTGAAGAGCATCGCTTAAGAGAATATTTTGAACAGTATGGGAAAATTGAAGTGATTGAA
ATCATGACTGACTGAGGCAGTGGCAAGAAGAGGGGCTTTGCTTTTGTTACCTTTGATGACCATGATTCTGTGGATAAGGT
TGTCATTCAGAAACACCATATTGTGAATGGCCACAACTGTGAAATAAGGAAAGCCCTGTCAAAGCAAGAGACAGACAGCT
AGTGCTTCATCCGGCCAAAGAGGTCAAAGTGGTTCTGGAAACTTTGGTGGGGGTTGTGGATGTGGTTTTGGTGGAAATGA
CAACTTTGGCTGTGGAGGAAACTTC

Alignment

ORF - retro_ogar_3215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 58.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGHDPKEPEQLRKLFIGGLSFETTDD-SLREQEHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSCVEEVD
          ....PKEPEQLRKLFI.GLSFE.TD..SLR...HFE.WGTLTDC.VMRDP.TKRSRGFGFVT....EEVD
Retrocopy KSESPKEPEQLRKLFIEGLSFEKTDK>SLRS--HFEQWGTLTDCEVMRDPNTKRSRGFGFVTNAALEEVD

Parental  AAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMED
          AAM.ARPHK.DGRVVEPKRAVSREDS..PGAHL.V.KIFVGGI.ED.EE..LR.YFE.YGKIE.IE.M.D
Retrocopy AAMNARPHKMDGRVVEPKRAVSREDS*RPGAHLPV*KIFVGGIEEDIEEHRLREYFEQYGKIEVIEIMTD

Parental  RQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQS-AGSQRGRG-GGSGNFMGRGG
          ..SGKKRGFAFVTFDDHD.VDK.V.QK.H..NGHNCE..KALSKQE..S...S...RG..GSGNF.G..G
Retrocopy *GSGKKRGFAFVTFDDHDSVDKVVIQKHHIVNGHNCEIRKALSKQETDS>SASSGQRGQSGSGNFGGGCG

Parental  NFGGGGGNFGRGGNF
          ...GG..NFG.GGNF
Retrocopy CGFGGNDNFGCGGNF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_3215 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii 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 18 parental genes, and 62 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	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Otolemur garnettii	ENSOGAG00000015353	3 retrocopies	retro_ogar_1384, retro_ogar_3077, retro_ogar_3189,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
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,
Otolemur garnettii	ENSOGAG00000029707	3 retrocopies	retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Otolemur garnettii	ENSOGAG00000030251	2 retrocopies	retro_ogar_3509, retro_ogar_385,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pteropus vampyrus	ENSPVAG00000010380	2 retrocopies	retro_pvam_1077, retro_pvam_326,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518,
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,