RetrogeneDB ID: retro_ocun_1772

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018880:260937..261575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000014806
• Aliases: None
• Description: None

Sequence

>retro_ocun_1772
GGCGGCTCTGGCACGACCACCTTCGCTGGGACGTTGGCCGCCCCTCTGCAAAGCAATGGCAGTGAGGGGCGGCAAGCAGA
GGAAGCAGGAAATCCACCGGAGGTCTGCTCGGCTGAGAAACACTAAGTACAAACCCGCTCCAGAGACTGAAAAAAAAAGT
GTCCACTAAAGGAAAAGGAAGAAAGCATATTTTTAAATTAAAAAACCCCATCAAAGCTCCTGCGTCGGTTTCTACCATAA
TCACTGCCCGAGTCCATCTTCTACAATGGTGTGTAGTACCAAACTGGAGACATTGTTTCTGTGACTGATGAGCAGGATGG
AAAGCCCTACTGTTCTCAGATCAGGGGTTTCATCCAGGACTAGTACTGCGAGAAGAGTGTGGCTCTGATGCGGCTCATTC
CCACTCTCTCCAGCCCCAGCCCCAGAGACCGGTTTGATCCTGCACCCTATATCATAGGGCCAGAAGAAGATCTTCCAAGG
ACGATGGAATACTCGGAGTGTCATTCACTTCTGAGTATTTCAAGCCATGGTCGTCGTCATTTCCTGCGGTTCCTACTAGA
CCTGAGAAGGGCTGTATAGGGACTCACGTTGGACCTACTCCTGCTATAACTGTCAAGGAAACAGTTGCCAACCGTTTG

Alignment

ORF - retro_ocun_1772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.36 %
• Parental protein coverage: 78.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GGFGATTFASTSAAPPQSNGGGG-GKQSKQEIHRRSARLRNTKYKSAPAAEKK-VSTKGKGRRHIFKLKN
          GG.G.TTFA.T.AAP.QSNG..G.GKQ.KQEIHRRSARLRNTKYK.AP..EKK.VSTKGKGR.HIFKLKN
Retrocopy GGSGTTTFAGTLAAPLQSNGSEG>GKQRKQEIHRRSARLRNTKYKPAPETEKK>VSTKGKGRKHIFKLKN

Parental  PIKAPESVSTIITA-ESIFYKGVYYQIGDVVSVIDEQDGKPYYAQIRGFIQDQYCEKSAALTWLIPTLS-
          PIKAP.SVSTIITA.ESIFY.GV.YQ.GD.VSV.DEQDGKPY..QIRGFIQD.YCEKS.AL..LIPTLS.
Retrocopy PIKAPASVSTIITA>ESIFYNGV*YQTGDIVSVTDEQDGKPYCSQIRGFIQD*YCEKSVALMRLIPTLSS

Parental  -SPRDRFDPASYIIGPEEDLPRKMEYLEFVCHA-PSEYFKSRSSPFPTVPTRPEKGYIWTHVGPTPAITI
          .SPRDRFDPA.YIIGPEEDLPR.MEY.E..CH...SEYFK..SS.FP.VPTRPEKG.I.THVGPTPAIT.
Retrocopy PSPRDRFDPAPYIIGPEEDLPRTMEYSE--CHS<TSEYFKPWSSSFPAVPTRPEKGCIGTHVGPTPAITV

Parental  KETVANHL
          KETVAN.L
Retrocopy KETVANRL

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	13.96 RPM
SRP017611_kidney	0.00 RPM	18.95 RPM
SRP017611_liver	0.00 RPM	4.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1772 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1772 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1772 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000193	2 retrocopies	retro_chof_2074, retro_chof_2604,
Dipodomys ordii	ENSDORG00000005895	10 retrocopies	retro_dord_267, retro_dord_270, retro_dord_300, retro_dord_318, retro_dord_363, retro_dord_459, retro_dord_463, retro_dord_504, retro_dord_551, retro_dord_566,
Monodelphis domestica	ENSMODG00000010701	1 retrocopy	retro_mdom_877,
Oryctolagus cuniculus	ENSOCUG00000014806	1 retrocopy	retro_ocun_1772 ,