RetrogeneDB ID: retro_ocun_1800

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018921:256675..257276(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026860
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPAB
• Ensembl ID: ENSOCUG00000026424
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A/B [Source:HGNC Symbol;Acc:5034]

Sequence

>retro_ocun_1800
AAGAACTAGGAGGACAAGGGGAAAATGTTCGTTGGTGGTCTGAGCTGGGATATCAACAACAAGATTTAAAGGACTATTTT
ACTAAGTTTGGCGAGGTCGTTGACTGCACAATAAAAGTGGATCCCAACACTGGATGGTCAAGAGGATTTGGGTTTATCCT
CTTCAAAGACGCAACCAGTGTGGAGAAGGTCCTAGATCAGAAGGTGCACAGGCTGGATGGCCATGTCATTGACCCTAAAA
GGCCATGGCTATGAAGAAGGACCCAGTGAAGAAGATGTTTGTGGGGGGTCTGAATCCTGAAGCTACTGAGGAAAAGATCA
GGGAGTGCTTTGGCGAGTTTGGGGAGATTGAGGCCATTGAGCTTCCAATGGATCCAAAGTCGAACAAAAGATGGAGTTTT
GCTTTTATTACCTTCAAAGAAGAAGACCCCATGAAGAAGGTTCTGGAGAAAAAGTTCCATACCATCAGTGGAAGCAAGTG
TGAAATCAAGGTGGCCCAGCCCAAGGAGGTCTATCAGCAGCAGCAGTATGGCTCTGGGGGCCGCGGGAACCGCGGCCGGG
GGAGCCGAGGCAGTGGTGGCAGCGGTGGAGGTAGAGGTCAG

Alignment

ORF - retro_ocun_1800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.78 %
• Parental protein coverage: 74.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QNEEDAGKMFVGGLSWDTSKK-DLKDYFTKFGEVVDCTIKMDPNTGRSRGFGFILFKDATSVEKEQVLDQ
          .N.ED.GKMFVGGLSWD...K.DLKDYFTKFGEVVDCTIK.DPNTG.SRGFGFILFKDATSVEK..VLDQ
Retrocopy KN*EDKGKMFVGGLSWDINNK<DLKDYFTKFGEVVDCTIKVDPNTGWSRGFGFILFKDATSVEK--VLDQ

Parental  KEHRLDGRVIDPK-KAMAMKKDPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELPMDPKSNKRRGFVF
          K.HRLDG.VIDPK.KAMAMKKDPVKK.FVGGLNPEATEEKIRE.FGEFGEIEAIELPMDPKSNKR..F.F
Retrocopy KVHRLDGHVIDPK<KAMAMKKDPVKKMFVGGLNPEATEEKIRECFGEFGEIEAIELPMDPKSNKRWSFAF

Parental  ITFKEEDPVKKVLEKKFHTISGSKCEIKVAQPKEVYQQQQYGSGGRGNRSRGSRGSGGGGGGGGQ
          ITFKEEDP.KKVLEKKFHTISGSKCEIKVAQPKEVYQQQQYGSGGRGNR.RGSRGSGG.GGG.GQ
Retrocopy ITFKEEDPMKKVLEKKFHTISGSKCEIKVAQPKEVYQQQQYGSGGRGNRGRGSRGSGGSGGGRGQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	2.26 RPM	151.38 RPM
SRP017611_kidney	2.64 RPM	164.81 RPM
SRP017611_liver	1.00 RPM	79.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1800 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1800 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 22 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	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Oryctolagus cuniculus	ENSOCUG00000026424	3 retrocopies	retro_ocun_1800 , retro_ocun_1811, retro_ocun_950,
Oryctolagus cuniculus	ENSOCUG00000026859	2 retrocopies	retro_ocun_1205, retro_ocun_642,
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,