RetrogeneDB ID: retro_ocun_894

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:32024885..32026104(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YES1
• Ensembl ID: ENSOCUG00000005874
• Aliases: None
• Description: v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 [Source:HGNC Symbol;Acc:12841]

Sequence

>retro_ocun_894
GAAAGTGGCTATATCCCTAGCAATTATGTAGCACCTGTGGATTCCATTCAGGCGGAAGAATGGTATTTTGGAAAAATGAG
GAGAAAAGATGTGAAAGATAGTACTTCTGAATCCTGGGAATCAGCGAGGTATATTTTTAGTGAGAGAGAGTGAAACTACT
AAAGGTGCTTATTCCCTCTCTATTTGTGATTGGGATGAGGTAAGGGGTGATAATGTGAAACACTACAAAATTATGAAACT
TGACAATAGTGGATATTACCTTACAACCAGAGCACAATTTTATACTCTTTAAAAATTGGTGAAACACTACACAGAACATG
CTGATGGTTTATGTCACAAGTTAACAACTGTGTGTTCAACTGTGGAACCACAGACTCAAGGTCTAGCAAAAGATGCTTGG
GAAATTCCTTGAGAATCTTTGAGACTAGAAGTTAAACTAGGACAAGGATGGTTTAGTGAAGTATGGGTGGGAACATGGAA
TGGAACCACAAAGGTAGCAATCAAAACACTAAAGCCAGGTACAATGATGCCAGAAGCTTTCTTCCAAGAAGCTCAGATAA
TGAAAAAATTAAGACACGATAAACTTGTTCCACTATATGCTGTTGTTTCTGAAGAACCAATTTATATAGTCACTGAATTT
ACATCAAAAGGGAGCTTATTAGATTTCCTTAAGGAAAGGGATGGAAAGTGTATGAAGCTTCCACAACTGGTTGATATGGC
TGCTCAGATTGCTGATGGCATGGCATATATTGAAAGAATGAACTATATTCACCAAAATCTTCGAGCTGCTAATATTCTTG
TAGGAGAAAATCTTGTATGCAAAATCGCAGATTTTGGTTTAGTGAGATTAATCGAAGACAATGAATACACAGCAAGACAA
GGTGCAAAATTTCCAATCAAATGGAAAGCTCCTGAGGCAGCACTGTATGGTTGATTTACAATCAAGTCTGATGTATGGTC
ATTTGGAATTCTACAGACAGAACTGGCTACAAAGGGCAGAGTACCATATCCAGGTATGGTGAACTGGGAAGTGCTGGAGC
AGGTGGAACAAGGATACAGGATGCCCTGCTCTCCAGACTGCCCAGAATCCCTCCAGGAATTGATGAATCTGTGTTAGAAG
AAGGACCCTGACGAAAGACCAACATCTGAGTATATTCAGTCTTTCCTGGAAGACTACTTCACTGCTCCAGAGCCACAGTA
CCAGTCAGGAGAAAATCTA

Alignment

ORF - retro_ocun_894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 75.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNGYIPSNYVAPADSIQAEEWYFGKMGRKDAER-LLLNPGNQRGIFLVRESETTKGAYSLSIRDWDEVRG
          ..GYIPSNYVAP.DSIQAEEWYFGKM.RKD.....LLNPGNQRGIFLVRESETTKGAYSLSI.DWDEVRG
Retrocopy ESGYIPSNYVAPVDSIQAEEWYFGKMRRKDVKD>VLLNPGNQRGIFLVRESETTKGAYSLSICDWDEVRG

Parental  DNVKHYKIRKLDNGGYYITTRAQFDTLQKLVKHYTEHADGLCHKLTTVCPTVKPQTQGLAKDAWEIPRES
          DNVKHYKI.KLDN.GYY.TTRAQF.TL.KLVKHYTEHADGLCHKLTTVC.TV.PQTQGLAKDAWEIP.ES
Retrocopy DNVKHYKIMKLDNSGYYLTTRAQFYTL*KLVKHYTEHADGLCHKLTTVCSTVEPQTQGLAKDAWEIP*ES

Parental  LRLEVKLGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFLQEAQIMKKLRHDKLVPLYAVVSEEPIYI
          LRLEVKLGQG.F.EVW.GTWNGTTKVAIKTLKPGTMMPEAF.QEAQIMKKLRHDKLVPLYAVVSEEPIYI
Retrocopy LRLEVKLGQGWFSEVWVGTWNGTTKVAIKTLKPGTMMPEAFFQEAQIMKKLRHDKLVPLYAVVSEEPIYI

Parental  VTEFMSKGSLLDFLKEGDGKYLKLPQLVDMAAQIADGMAYIERMNYIHRDLRAANILVGENLVCKIADFG
          VTEF.SKGSLLDFLKE.DGK..KLPQLVDMAAQIADGMAYIERMNYIH..LRAANILVGENLVCKIADFG
Retrocopy VTEFTSKGSLLDFLKERDGKCMKLPQLVDMAAQIADGMAYIERMNYIHQNLRAANILVGENLVCKIADFG

Parental  LARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILQTELVTKGRVPYPGMVNREVLEQVE
          L.RLIEDNEYTARQGAKFPIKW.APEAALYG.FTIKSDVWSFGILQTEL.TKGRVPYPGMVN.EVLEQVE
Retrocopy LVRLIEDNEYTARQGAKFPIKWKAPEAALYG*FTIKSDVWSFGILQTELATKGRVPYPGMVNWEVLEQVE

Parental  RGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEPQYQPGENL
          .GYRMPC...CPESL.ELMNLC.KKDPDERPT.EYIQSFLEDYFTA.EPQYQ.GENL
Retrocopy QGYRMPCSPDCPESLQELMNLC*KKDPDERPTSEYIQSFLEDYFTAPEPQYQSGENL

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	11.37 RPM
SRP017611_kidney	0.10 RPM	23.11 RPM
SRP017611_liver	0.08 RPM	8.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_894 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_894 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176105	1 retrocopy	retro_hsap_2551,
Monodelphis domestica	ENSMODG00000021477	1 retrocopy	retro_mdom_1121,
Oryctolagus cuniculus	ENSOCUG00000005874	1 retrocopy	retro_ocun_894 ,
Otolemur garnettii	ENSOGAG00000003375	1 retrocopy	retro_ogar_1684,
Pan troglodytes	ENSPTRG00000009824	1 retrocopy	retro_ptro_1487,