RetrogeneDB ID: retro_ocun_747

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:46887878..46888476(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSOCUG00000017448
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 (VBP1), mRNA [Source:RefSeq mRNA;Acc:NM_001171386]

Sequence

>retro_ocun_747
CCCAACATGGCGGCCGCTAAGGACGGTTGTGGCATGGAAGTGACCGCGGGGAACGGGCGGCGGCTTCACCTGGGGATTCC
TGAGGCAGTATTTATGGAAGATGTAGATTCCTTCATGAAACAGCCTGGGAATGAGACTGCAGATACAGTACTAAAGAAGC
TGGATGAGCAGTACCAGAAGTATAAATTTATGGAACTCAATCTTGCTCAAAAGAAACGGAGGCTAAAGGGTCAGATTCCT
GAAATTAAGCAGACTTTGGAAATTTTAAAATACATGCATGCAGAAGAAAAAAGAGTCCACCAGTTCACTGGAGACCAGGT
TCTTATTGGCAGATAATCTGTACTGCAAAGCTTCAGTTCCTCCCACTGATAAAGTGTGTCTGTGGTTGGGGGCTAATGTT
GTGCTTGAATATGACATTGATGAAGCTCAGGCTTTGTTGGAAAAGAATTTATTGACAGCCACAAAGAATCTTGATTCTCT
TGAAGAAGACCTTGACTTTCTTCGAGATCAATTTACTACCACAGAAGTCAATATGGCCAGGGTTTATAATTGGGATGTAA
AAAGAAGAAACAAAGATGATTCTGCCAAGAACAAAGTG

Alignment

ORF - retro_ocun_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.0 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PNMAAAKDGCGMEVTAGNGRRLHLGIPEAVFVEDVDSFMKQPGNETADTVLKKLDEQYQKYKFMELNLAQ
          PNMAAAKDGCGMEVTAGNGRRLHLGIPEAVF.EDVDSFMKQPGNETADTVLKKLDEQYQKYKFMELNLAQ
Retrocopy PNMAAAKDGCGMEVTAGNGRRLHLGIPEAVFMEDVDSFMKQPGNETADTVLKKLDEQYQKYKFMELNLAQ

Parental  KKRRLKGQIPEIKQTLEILKYM-QKKK-ESTSSLETRFLLADNLYCKASVPPTDKVCLWLGANVMLEYDI
          KKRRLKGQIPEIKQTLEILKYM...KK.ESTSSLETRFLLADNLYCKASVPPTDKVCLWLGANV.LEYDI
Retrocopy KKRRLKGQIPEIKQTLEILKYM>MQKKKESTSSLETRFLLADNLYCKASVPPTDKVCLWLGANVVLEYDI

Parental  DEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEVNMARVYNWDVKRRNKDDSAKNKV
          DEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEVNMARVYNWDVKRRNKDDSAKNKV
Retrocopy DEAQALLEKNLLTATKNLDSLEEDLDFLRDQFTTTEVNMARVYNWDVKRRNKDDSAKNKV

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	0.11 RPM	12.69 RPM
SRP017611_kidney	0.00 RPM	16.12 RPM
SRP017611_liver	0.08 RPM	4.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_747 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_747 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_747 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Echinops telfairi	ENSETEG00000017655	2 retrocopies	retro_etel_2085, retro_etel_552,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Loxodonta africana	ENSLAFG00000016507	2 retrocopies	retro_lafr_1200, retro_lafr_163,
Myotis lucifugus	ENSMLUG00000015396	3 retrocopies	retro_mluc_1600, retro_mluc_2019, retro_mluc_986,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747 ,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,