RetrogeneDB ID: retro_ogar_3509

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL874018.1:35219..35964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSOGAG00000030251
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A/B [Source:HGNC Symbol;Acc:5034]

Sequence

>retro_ogar_3509
GCAGCGCCCCGGAGCGGGAATCAGAACGGCGCCGAGGGTGACCAGATCAACACCAGCAAGAACGAGGAGGACGCGGGGAA
AATGTTTGTCGGTGGTCTGAGTTGGGATATCAGTAAGAAAGATTTAAAAGACTATTTTACTAAATTTGGAGAGAACGTTG
ACTGTACATTAAAAATGGATCCCAACACTGGATGATCAAGAGGGTTTGGGTTTATCCTCTTCAGAGATGCAGCCAGTGTG
GAGAAGGTCCTAGACCAGAAGGAACACAGGCTGGATGGTCCTGTCATTGATCCTAAAAAGGCAATGGCGGCTATGAAGAA
GGACCCAGTAAAGAGAATCTTTGTGTGTGTGTGTGTGGGGGGTCTGAATCCTGAAGCTACTGAGGAAAAGATCAGGGAGT
ACTTTGGAGACTTTGGGGAGATTGAAGCCATTGAGCTTCCAAATGGATCCAAAGTTGAACAAGAGATGAAGTTTTGTTTT
TATCACCTTTAAAGAAGAAGAACCTGTGAAGAAGGTTCTGGAAAAAAAGTTCCATATTATCAGTGGAAGCAAGTGTGAAA
TCGAGGTGGCCCAGCCCAAAGACGTCTATCAGCAGCAGCAGTATGGCTCTGGGGGCCGTGGAAACTGCAACCGGGGGAAC
CGAGGCAGCGGTGGCGGCGGTGGTGGTGGATGTCAGGGCAGTACAAACTATGGCAAGAGCCAGCGACGTGGTGACCATCA
GAATAATTTCAAACCATACCAAGGC

Alignment

ORF - retro_ogar_3509 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.12 %
• Parental protein coverage: 74.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAPPSGNQNGAEGDQINASKNEEDAGKMFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKMDPNTGRSRGFG
          AAP.SGNQNGAEGDQIN.SKNEEDAGKMFVGGLSWD.SKKDLKDYFTKFGE.VDCT.KMDPNTG.SRGFG
Retrocopy AAPRSGNQNGAEGDQINTSKNEEDAGKMFVGGLSWDISKKDLKDYFTKFGENVDCTLKMDPNTG*SRGFG

Parental  FILFKDAASVEKVLDQKEHRLDGRVIDPKKAM-AMKKDPVKKIFVGGLNPEATEEKIREYFGD-FGEIEA
          FILF.DAASVEKVLDQKEHRLDG.VIDPKKAM.AMKKDPVK.I...........E...E.....FG....
Retrocopy FILFRDAASVEKVLDQKEHRLDGPVIDPKKAMAAMKKDPVKRIXXXXXXGGLNPEATEEKIREYFGDFGE

Parental  IE---LPMDPK-LNKRRGFVFITFKEEEPVKKVLEKKFHTISGSKCEIKVAQPKEVYQQQQYGSGGRGNR
          IE...LP...K.LNKR..FVFITFKEEEPVKKVLEKKFH.ISGSKCEI.VAQPK.VYQQQQYGSGGRGN.
Retrocopy IEAIELPNGSK>LNKR*SFVFITFKEEEPVKKVLEKKFHIISGSKCEIEVAQPKDVYQQQQYGSGGRGNC

Parental  NRGNRGSGGGGGGGGQSQSWNQGYGNYWNQGYGYQQGYGPGYG
          NRGNRGSGGGGGGG.Q.......YG.....G...Q....P..G
Retrocopy NRGNRGSGGGGGGGCQGST---NYGKSQRRG-DHQNNFKPYQG

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_3509 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 15 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000241	2 retrocopies	retro_cfam_408, retro_cfam_412,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Loxodonta africana	ENSLAFG00000001189	1 retrocopy	retro_lafr_405,
Macropus eugenii	ENSMEUG00000007909	2 retrocopies	retro_meug_169, retro_meug_246,
Myotis lucifugus	ENSMLUG00000003380	2 retrocopies	retro_mluc_2024, retro_mluc_2138,
Nomascus leucogenys	ENSNLEG00000015775	1 retrocopy	retro_nleu_1611,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800, retro_ocun_1811, retro_ocun_950,
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,
Pongo abelii	ENSPPYG00000016107	1 retrocopy	retro_pabe_821,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,