RetrogeneDB ID: retro_ocun_950

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:58308953..58309558(-)
• Located in intron of: None

Retrocopy information

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

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_950
AAAATGTTCCTTAGTGGTCTGAGCTGGAATACCAGCAAAAAAAGATTTAGAGGACCATTTTTAAGTTTAGAGAGATCATT
GATTACACAATAAAAATAGATCCCAACAGTGGATAGTCAAGAGGATTTGGGTTTATCCTCTTCAAAGACGCAAGCAGTGT
GGTGTGGAGAAGGTCCTGGACCAGAAAGAGCACAGGCTGGATGGCCATGTCACTGACCCTGAAAAGGCCTTGACTATGAA
AAAAGACCCAGTGAAAGCAGTATTTGTGGGCAGTCTGAATCCTGAAGCTGTTGAGGGAAATATGGACAAGTACTTTGACA
AGTTTGGCTAGATTGAGACCATTAAGCGTCATTAAGTATATCCAGTGTTGAACAAAAGACAGGGTCTTTTTTTAATCACC
TTTAAATCACACCCCTTGAAAAGGGTTCTGGCGAAGTGGTTTCCACCTCAGTGGAAATAAGTGTGAAATCAAGGTGGCCC
AGCCCAAAGAGATCTAGCAGCAGTGACAGTGTGGCTCCGGGAGCTACAGAAACTGCCACCTGGGGAAGTGAGACATTGGT
GGCTGCAGTGGACGTGGTCAGGGTAGAGCAAATTACTGGGAAGAA

Alignment

ORF - retro_ocun_950 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.97 %
• Parental protein coverage: 74.54 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KMFVGGLSWDTSKKDLKDYFT-KFGEVVDCTIKMDPNTGRSRGFGFILFKDATSVE-KEQVLDQKEHRLD
          KMF..GLSW.TSKK.....F..KF.E..D.TIK.DPN.G.SRGFGFILFKDA.SV...E.VLDQKEHRLD
Retrocopy KMFLSGLSWNTSKKRFRGPFL<KFREIIDYTIKIDPNSG*SRGFGFILFKDASSVV<VEKVLDQKEHRLD

Parental  GRVIDPKKAMAMKKDPVKKIFVGGLNPEATEEKIREYFGEFGEIEAIELP-MDPKSNKRRGFVFITFKEE
          G.V.DP.KA..MKKDPVK..FVG.LNPEA.E.....YF..FG.IE.I......P..NKR.G...ITFK..
Retrocopy GHVTDPEKALTMKKDPVKAVFVGSLNPEAVEGNMDKYFDKFG*IETIKRH*VYPVLNKRQGLFLITFKSH

Parental  DPVKKVLEK-KFHTISGSKCEIKVAQPKEVYQQQQYGSGGRGNRSRGSRGSGG-GGGGGGQSQSWNQ
          .P.K.VL.K..FH..SG.KCEIKVAQPKE..QQ.Q.GSG...N...G....GG..G.G.G....W..
Retrocopy -PLKRVLAK>GFH-LSGNKCEIKVAQPKEI*QQ*QCGSGSYRNCHLGK*DIGGCSGRGQGRANYWEE

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	0.00 RPM	151.38 RPM
SRP017611_kidney	0.00 RPM	164.81 RPM
SRP017611_liver	0.00 RPM	79.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_950 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_950 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_950 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,