RetrogeneDB ID: retro_ocun_1463

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:15178262..15178787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAQ
• Ensembl ID: ENSOCUG00000010482
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide (YWHAQ), mRNA [Source:RefSeq mRNA;Acc:NM_001082168]

Sequence

>retro_ocun_1463
AGGGTCATCTCGAGCTTCCTGCAGAAGACCCATACCTCCGACAAGAAACTGCAGCTCAGCAAGGACTACCGGGAGAAGGT
GGAGTCGGAGCTGCGGTCCATCTGCACCTCGGTGCTGCAGTTGTTGGAGAAGTATTTGATAGCCAATGCAACTAATCCAG
AGAGTAAGGTCTTCTATCTGAAAATGAAGGGAGATTACTTCGGGTACCTTGCTGAAGTTGCATGTGGTGATGATCAAAAA
CAAACGATAGATAATTCCCATGGAGCTTACCAAGAGGCATTTGTTATGAGCAAGAAAGAGATGCAACCCACACACCCAAT
CTGCCTGGGGCTGGCTCTGGACATTTCTGTATTTTACTATGGGATCCTTAATAACCCAGAGCTTGCCTGCACAATGACTT
AAACAGCTTTTGATGAGGCCATTGCAGAACTCGACACACTTAATGAAGACTCCTACAAAGAGAGCACCCTCATGCAGTTG
CTTAGAGACAATTTAACATTATGGACATCAGACAGAGCAGCAGAG

Alignment

ORF - retro_ocun_1463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.8 %
• Parental protein coverage: 71.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVISSIEQKTDTSDKKLQLIRDYREKVESELRAICTTVLELLDKYLIANATNPESKVFYLKMKGDYFRYL
          RVISS..QKT.TSDKKLQL..DYREKVESELR.ICT.VL.LL.KYLIANATNPESKVFYLKMKGDYF.YL
Retrocopy RVISSFLQKTHTSDKKLQLSKDYREKVESELRSICTSVLQLLEKYLIANATNPESKVFYLKMKGDYFGYL

Parental  AEVACGDDRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKTAFDEA
          AEVACGDD.KQTIDNS.GAYQEAF..SKKEMQPTHPI.LGLAL..SVFYY.ILNNPELACT...TAFDEA
Retrocopy AEVACGDDQKQTIDNSHGAYQEAFVMSKKEMQPTHPICLGLALDISVFYYGILNNPELACTMT*TAFDEA

Parental  IAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGE
          IAELDTLNEDSYK.STL.MQLLRDNLTLWTSD.A.E
Retrocopy IAELDTLNEDSYKESTL-MQLLRDNLTLWTSDRAAE

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	0.33 RPM	213.03 RPM
SRP017611_kidney	0.20 RPM	107.34 RPM
SRP017611_liver	0.39 RPM	18.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1463 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1463 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008618	4 retrocopies	retro_amel_1214, retro_amel_1382, retro_amel_1837, retro_amel_917,
Bos taurus	ENSBTAG00000002108	2 retrocopies	retro_btau_1180, retro_btau_86,
Callithrix jacchus	ENSCJAG00000006394	2 retrocopies	retro_cjac_2197, retro_cjac_3127,
Cavia porcellus	ENSCPOG00000011321	4 retrocopies	retro_cpor_135, retro_cpor_1463, retro_cpor_616, retro_cpor_668,
Equus caballus	ENSECAG00000004925	1 retrocopy	retro_ecab_134,
Echinops telfairi	ENSETEG00000015359	4 retrocopies	retro_etel_1027, retro_etel_1048, retro_etel_235, retro_etel_65,
Felis catus	ENSFCAG00000007854	2 retrocopies	retro_fcat_1702, retro_fcat_771,
Homo sapiens	ENSG00000134308	2 retrocopies	retro_hsap_3004, retro_hsap_8,
Gorilla gorilla	ENSGGOG00000001569	1 retrocopy	retro_ggor_2081,
Myotis lucifugus	ENSMLUG00000005383	1 retrocopy	retro_mluc_1817,
Monodelphis domestica	ENSMODG00000014740	1 retrocopy	retro_mdom_1339,
Mustela putorius furo	ENSMPUG00000013252	2 retrocopies	retro_mputfur_1132, retro_mputfur_730,
Mus musculus	ENSMUSG00000076432	10 retrocopies	retro_mmus_1076, retro_mmus_1378, retro_mmus_1926, retro_mmus_2250, retro_mmus_2299, retro_mmus_2471, retro_mmus_2689, retro_mmus_3250, retro_mmus_3308, retro_mmus_406,
Nomascus leucogenys	ENSNLEG00000013534	3 retrocopies	retro_nleu_2543, retro_nleu_750, retro_nleu_869,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Oryctolagus cuniculus	ENSOCUG00000003002	1 retrocopy	retro_ocun_273,
Oryctolagus cuniculus	ENSOCUG00000010482	1 retrocopy	retro_ocun_1463 ,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Otolemur garnettii	ENSOGAG00000000547	3 retrocopies	retro_ogar_1047, retro_ogar_1732, retro_ogar_39,
Pongo abelii	ENSPPYG00000012663	4 retrocopies	retro_pabe_1165, retro_pabe_2490, retro_pabe_3391, retro_pabe_3511,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pteropus vampyrus	ENSPVAG00000005334	1 retrocopy	retro_pvam_983,
Rattus norvegicus	ENSRNOG00000008104	5 retrocopies	retro_rnor_1569, retro_rnor_2065, retro_rnor_2123, retro_rnor_2180, retro_rnor_2746,
Sorex araneus	ENSSARG00000012476	4 retrocopies	retro_sara_1, retro_sara_162, retro_sara_179, retro_sara_23,
Tursiops truncatus	ENSTTRG00000000871	4 retrocopies	retro_ttru_1006, retro_ttru_1109, retro_ttru_1530, retro_ttru_1536,