RetrogeneDB ID: retro_ogar_600

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873524.1:33706662..33707457(+)
• Located in intron of: ENSOGAG00000033583

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_600
GGACGAGGCGAGTCCAGTCTCAAAATGAAGGGCCATGATGCAAAGGAACCAGAGCAGGTGAGAAAATTGTTTCTTGGTGG
TCTGAGCTTTGAAACTACAGATGACAATTTAAGAGAATACTTTGAGAAATAGGGCACACTCACAGATTGTGTGGTAGTGC
AAGATCCCCAAACAAAATGTTCCAGGGGCTTTGGTTTTATGACTTACTCTTGTGTAGAAGAGGTGGATGCAGTAATGTGT
GCCTGACCACACAAGGTTGATGGGCATGTTGTGGAACCAAAGAGAGGTGTTTCTCGAGAGGATTCTGTAAAGCCTGGTGC
CCATCTCACAGTGAAGAAAATTTTTGTTGGTGGTATTAAAGAAGATACAGAAGAATATAATTTGAGAGACTACTTTGAAA
AGTATGGCAAGATTGAAACCATAGAAGTTATGGAAGACAGGCAGAGTGGAAAAAAGAGAGGATTTGCTTTTGTAACTTTT
GATGATCATGACACTGTTGATAAAATTGTTGTTCAGAAATACCACACTATTAATGGGTAAAACTGTGAAGCAAAAAAGGC
CCTTTCTAAACAAGAGATGCAGTCTGCTGGATCGCAAAGAGGTTGTGGAGGTGGAACTGGCAACTTTATGGGTCGGGAAG
GAAACTTTGGAGGTGGTGGAGGAAATTTTGGTTGTAGTGGAAACTTTGATGGAAGAGGAGGATATGGTGGTAGAGGTGGT
GGCAGCCCATGTAGTTATGGATAAGGTGATGGTGGATACAATGGATTTGGAGGTGACAGTGGGAACTATGGCAGT

Alignment

ORF - retro_ogar_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.52 %
• Parental protein coverage: 69.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRRRRRRGEEGHDPKEPEQLRKLFIGGLSFETTDDSLREQEHFEKWGTLTDCVVMRDPQTKRSRGFGFVT
          GR........GHD.KEPEQ.RKLF.GGLSFETTDD.LRE...FEK.GTLTDCVV..DPQTK.SRGFGF.T
Retrocopy GRGESSLKMKGHDAKEPEQVRKLFLGGLSFETTDDNLRE--YFEK*GTLTDCVVVQDPQTKCSRGFGFMT

Parental  YSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKI
          YSCVEEVDA.MCA.PHKVDG.VVEPKR.VSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKI
Retrocopy YSCVEEVDAVMCA*PHKVDGHVVEPKRGVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKI

Parental  ETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQEMQSAGSQRGRGGGSGN
          ETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTING.NCE.KKALSKQEMQSAGSQRG.GGG.GN
Retrocopy ETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTING*NCEAKKALSKQEMQSAGSQRGCGGGTGN

Parental  FMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGFGGDGGGFES
          FMGR...............NF.GRGGYGG.GGGS..SYG.GDGGYNGFGGD.G...S
Retrocopy FMGRXXXXXXXXXXXXXXXNFDGRGGYGGRGGGSPCSYG*GDGGYNGFGGDSGNYGS

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_600 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,