RetrogeneDB ID: retro_ocun_82

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:5871862..5873350(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000698
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: XIAP
• Ensembl ID: ENSOCUG00000009878
• Aliases: None
• Description: X-linked inhibitor of apoptosis (XIAP), mRNA [Source:RefSeq mRNA;Acc:NM_001171325]

Sequence

>retro_ocun_82
ATGATGTTTAACAGCTTTGAAGGATCTAAAACGTGTGTGTCTGCAGACAGCAATAAAGATGAAGAATTTGTAGAAGAGTT
TAACAGATTAAGAACCTTCACTGGTTTTCCAAGTGATAGTCCTGTTTCAGCAGCAACACTGGCTCGAGCAGGGTTTCTAT
ATGCTGGAGAAGGAGACACTGTACGATGCTTTAGTTGTCGTGCAGCAGTGGACAGGTGCATGTACGGAGACTCAGCAGTT
GGAAGACACAGGGCAGTATCCCCAAATTGCAGATTTATCAATGGCTTTTATTTTGAAAACAGTGCCACACAACCTACAAA
TCCTGGTGTCCAAAATGGTGAATACAGAAGTGCAGACGACCTGGGAAACAGAAATCATTTTGCTTTGGACGGACCATCTG
AGACTCCTGCAGACCCTCCTTTGAGAACTGGACAGATTGTAGGTACCCCAGACACTGTATACCCGAGGAACCCTGAGATG
TGTAGTGAAGAAGCTAGATTAGAGTCCTTTCAGAACTGGCCAGATTATGTCCACTTAACTCCCAGAGAGTTAGCCAGTGC
TGGGCTCTACTACACAGGTATTGATGATCAAGTGCAGTGCTTTTGTTGTGGTGGAAAACTGAAAAACTGGGAACCTGGCA
ATCGTGCCTGGTCAGAACACAGGCAGCACTTTCCTACTTGCTTCTTTGTTGTGGGCAGGGGTGTTAATAATCAAAGTGAA
TTTAATATTGTGAGTTCTGATAGGAATTTCTCAGATTCAACAAATCCTCCAAGAAACCCAGCCATGGCAGATTATGCTGC
TCGGATCATTACTTTTGGATCATGGAGATACTCAGTTAACAAGGAGAAGCTTGCAAGAGCTGGATTGTACTGTTTAGGTG
AAGGTGATCAAGTAGAGTGCTTTCACTGTGGAGGGGGCTTAACTGACTGGGAGCCCAGTGATGATCCTTGGGAGCAACAT
GCTAAGTGGTATCCAGGGTGTGAATATGTATTAGAAAAGAAAGGACAAGGGTACATCAATAATATTCATCTGACCCATTC
ACTTAAGGAGTCTCCAGCAAGGGCTGCTGGGAAAATACCATCACTATCCGAAAGAATTGTTGATCCCATCTTCCAAAGTC
CTGTGGTACAAGAAACTCTGAGAATGGGATTCAGTTTCAGGGAGATTAAGAAAATGATGGAGGAAAAAGTACAGAGGTGT
GGGAGCAACTATAAATCACTTGAGGTTGCAGATCTAGTGACTGCTCAGAAAAACAGTCCACACGATGAATCAAGTCAGGC
TTCCTTGCAGAAAGAAGTTAGCACTGAAGAGCAGCTAAGGCGCCTGCAAGAGGAGCGGCTTTGCAAAATCTGTATGGACA
GAAATACTGCTGTTGTTTTTATTCCTTGTGGACATCTGGTCACTTGTAACACATGTGCTGAAGCAGTTGACAAATGTCCC
ATGTGCTACACAGTCATTACTTTCAAGCAAAAAATTTTTACATCTTAA

Alignment

ORF - retro_ocun_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTFNSFEGSKTCVPADINKDEEFVEEFNRLKTFANFPSSSPVSASTLARAGFLYTGEGDTVRCFSCHAAV
          M.FNSFEGSKTCV.AD.NKDEEFVEEFNRL.TF..FPS.SPVSA.TLARAGFLY.GEGDTVRCFSC.AAV
Retrocopy MMFNSFEGSKTCVSADSNKDEEFVEEFNRLRTFTGFPSDSPVSAATLARAGFLYAGEGDTVRCFSCRAAV

Parental  DRWQYGDSAVGRHRKVSPNCRFINGFYFENSAAQSTNPGVQNGQYKGENYLGNRNHFALDRPSETHADYL
          DR..YGDSAVGRHR.VSPNCRFINGFYFENSA.Q.TNPGVQNG.Y.....LGNRNHFALD.PSET.AD..
Retrocopy DRCMYGDSAVGRHRAVSPNCRFINGFYFENSATQPTNPGVQNGEYRSADDLGNRNHFALDGPSETPADPP

Parental  LRTGQVVDISDTIYPRNPAMCSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIDDQVQCFCCGGKLKNW
          LRTGQ.V...DT.YPRNP.MCSEEARL.SFQNWPDY.HLTPRELASAGLYYTGIDDQVQCFCCGGKLKNW
Retrocopy LRTGQIVGTPDTVYPRNPEMCSEEARLESFQNWPDYVHLTPRELASAGLYYTGIDDQVQCFCCGGKLKNW

Parental  EPCDRAWSEHRRHFPNCFFVLGRNVNIRSESDVVSSDRNFPNSTNPPRNPAMADYEARIISFGTWIYSVN
          EP..RAWSEHR.HFP.CFFV.GR.VN..SE...VSSDRNF..STNPPRNPAMADY.ARII.FG.W.YSVN
Retrocopy EPGNRAWSEHRQHFPTCFFVVGRGVNNQSEFNIVSSDRNFSDSTNPPRNPAMADYAARIITFGSWRYSVN

Parental  KEQLARAGFYALGEGDKVKCFHCGGGLTDWKPNEDPWEQHAKWYPGCKYLLEEKGQEYINNIHLTHSLEE
          KE.LARAG.Y.LGEGD.V.CFHCGGGLTDW.P..DPWEQHAKWYPGC.Y.LE.KGQ.YINNIHLTHSL.E
Retrocopy KEKLARAGLYCLGEGDQVECFHCGGGLTDWEPSDDPWEQHAKWYPGCEYVLEKKGQGYINNIHLTHSLKE

Parental  SLARTAENTPSQTKRIDDTIFQSPMVQEAIRMGFSFREIKKIMEEKVQMCGSNYKSLEVLVADLVNAQKS
          S.AR.A...PS...RI.D.IFQSP.VQE..RMGFSFREIKK.MEEKVQ.CGSNYKSLE..VADLV.AQK.
Retrocopy SPARAAGKIPSLSERIVDPIFQSPVVQETLRMGFSFREIKKMMEEKVQRCGSNYKSLE--VADLVTAQKN

Parental  STQDESSQTSLQKEVSTEEQLRRLQEEKLCKICMDRNIAVVFIPCGHLVTCKQCAEAVDKCPMCYTVITF
          S..DESSQ.SLQKEVSTEEQLRRLQEE.LCKICMDRN.AVVFIPCGHLVTC..CAEAVDKCPMCYTVITF
Retrocopy SPHDESSQASLQKEVSTEEQLRRLQEERLCKICMDRNTAVVFIPCGHLVTCNTCAEAVDKCPMCYTVITF

Parental  KQKIFMS
          KQKIF.S
Retrocopy KQKIFTS

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	0.50 RPM	25.28 RPM
SRP017611_kidney	0.00 RPM	20.27 RPM
SRP017611_liver	0.00 RPM	14.34 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_82 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_82 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_82 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006316	1 retrocopy	retro_cpor_1292,
Mus musculus	ENSMUSG00000025860	1 retrocopy	retro_mmus_3020,
Oryctolagus cuniculus	ENSOCUG00000009878	1 retrocopy	retro_ocun_82 ,
Otolemur garnettii	ENSOGAG00000025670	1 retrocopy	retro_ogar_2859,
Pongo abelii	ENSPPYG00000020696	1 retrocopy	retro_pabe_1682,
Pan troglodytes	ENSPTRG00000022247	1 retrocopy	retro_ptro_1381,