RetrogeneDB ID: retro_ocun_340

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:12117967..12119375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF14
• Ensembl ID: ENSOCUG00000016953
• Aliases: None
• Description: ring finger protein 14 [Source:HGNC Symbol;Acc:10058]

Sequence

>retro_ocun_340
TCAGAATATTAAGAGGCTCAGGAGGATGAACTGTTGGCCCTGGAGAGCATTTATGACAGAAGATGAATTGATAAAAGCCA
AGTCTGTCCAAAGCAGAGAAACCAGGATTATTTGGATTTGCCACAAAATTTCAAGATATTTGTGAGCAGCACTTCAGTGA
GTGTCTCCAGAATGGTGGCTCTCAATCCACCGTTGACTTTCTGCCTCACTTGTGCTGAACTTCGAGCTGCTACCAGATTA
TCCATCCTCCTCCCCACCTTCATTTACACTTAGTGGCAAGTGGCTGCCACCAGCTCAGCCGTCTGCTCTGTGCAGGCACG
CAGACAACCTGTGGAAGGAACACCTAGGCAGGTGGTCCTGTTTGCCCGGATGCAGTTTCTTAAGGAAGAGACCCTCGCAT
ACCAGAATACTGTCTCTCCTTTTGAACTCAAGATGGGATCTCAGAAAAAAAGCGCTCAGGCTTCTTCCAACAAAGAGTGG
AGTTTGGAGGAGCTGCTGGATCCGACGTAGACCAAGAGGAAGTCGTAGATGAGGGAGCTGTACAAGATGTGGAATCATTG
TCAAGTCTGATCCAGGAAACCTTGGACTTTGATCAAGCTCAGTAGATAAAATGCTTTAACAGTAAATTGTTGCTTTGCAA
TATCTGTTTCTGTGAGAAGCTGGGTGGTGAACGCATGTGCTTCTTGGAGTGCAGGCATGTGTATTGCAAAGCTTGCCTGA
AGGCCTACTTTGAAATCCAGATCAAAGATGGCCAAGTTCAGTGCCTCAACTGTCCAGAACCAAAGTGCCCTTCAGTGGCT
ACTCCTGGTCAGGTCAAGGAGCTGGTAGAAGCAGAATCATTTGCTTGCTTCAACTGCCTTGTCATGCAGTCCACCTTGGA
CCTGATGGCAGGCATGGTGTACTGCCCCTGCCCATGCTGCCAGCTGCTAGCTGCCTGTGATGCAGGAGCTGGGCTGCACC
ATGGGCATCTGCTCCGGGTGCAATTTTGCCTTCTGTATCTTGTGCAGATTGACCTACCACGGGGTCTCTGCTCCATGTAA
GGTGACTACAGAGAAACTGATAGACTTATGGAATGAGTCCCTGCAAGCAGATGAGACCAATAAAAGATTTTTGGAACAGA
GATATGATACGAGGGTTATTCAGAGGTCACTGGAAGAGATGGAGAGTAATGAGTGGCTGGAAAAGAACTCAGAGAGCTGC
CCCTGTTGTGGGGCCCCATACAGAAATTTGACGGCAGTAACAGATGATGTGTACTGGCTGTATGCAGTATTTCTGTGGGA
TTTGCATGGGTTTTCTCTCTGGAGCAAACCCTTAGCAACACTTCCCTGATCCTGATTCCCTGTGTTTCAATCAATTGTTC
CATACCATGGATGTAAATGGAGATATTTGGGAAGATGAGATTGAAGAC

Alignment

ORF - retro_ocun_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  SEDREAQDDELLALASIYDG-DEFRKAESVQGGETRI-YLDLPQNFKIFVSGNS-NECLQNSGFESTICF
          SE..EAQ.DELLAL.SIYD..DE..KA.SVQ..ETRI.YLDLPQNFKIFVS..S..ECLQN.G..ST..F
Retrocopy SEY*EAQEDELLALESIYDR>DELIKAKSVQSRETRI<YLDLPQNFKIFVSSTS<SECLQNGGSQSTVDF

Parental  LP-PLVLNFELPPDYPSSSPPSFTLSGKWLSPTQLSALCKHLDNLWEEHRG-SVVLFAWMQFLKEETLAY
          LP..LVLNFEL.PDYPSSSPPSFTLSGKWL.P.Q.SALC.H.DNLW.EH.G..VVLFA.MQFLKEETLAY
Retrocopy LP<SLVLNFELLPDYPSSSPPSFTLSGKWLPPAQPSALCRHADNLWKEHLG<QVVLFARMQFLKEETLAY

Parental  LNIVSPFELKMGSQKKVQRRTAQASSTKE-LEFGGATGSDVDQEEVVDERAVQDVESLSSLIQEILDFDQ
          .N.VSPFELKMGS....Q...AQASS.KE..EFGGA.GSDVDQEEVVDE.AVQDVESLSSLIQE.LDFDQ
Retrocopy QNTVSPFELKMGS----QKKSAQASSNKE<VEFGGAAGSDVDQEEVVDEGAVQDVESLSSLIQETLDFDQ

Parental  AQQTKCFNSKLFLCSICFCEKLGSECMYFLECRHVYCKACLKDYFEIQIKDGQVQCLNCPEPKCPSVATP
          AQ..KCFNSKL.LC.ICFCEKLG.E.M.FLECRHVYCKACLK.YFEIQIKDGQVQCLNCPEPKCPSVATP
Retrocopy AQ*IKCFNSKLLLCNICFCEKLGGERMCFLECRHVYCKACLKAYFEIQIKDGQVQCLNCPEPKCPSVATP

Parental  GQVKELVEAELFARYDRLLLQSSLDLMADVVY--CP-RPCCQLPVMQEPGCTMGICSSCNFAFCTLCRLT
          GQVKELVEAE.FA....L..QS.LDLMA..VY..CP....C.LPVMQE.GCTMGICS.CNFAFC.LCRLT
Retrocopy GQVKELVEAESFACFNCLVMQSTLDLMAGMVYCPCP>AASC*LPVMQELGCTMGICSGCNFAFCILCRLT

Parental  YHGVS-PCKVTAEKLIDLRNEYLQADEANKRFLEQRYGKRVIQKALEEMESKEWLEKNSKSCPCCGT-PI
          YHGVS.PCKVT.EKLIDL.NE.LQADE.NKRFLEQRY..RVIQ..LEEMES.EWLEKNS.SCPCCG..PI
Retrocopy YHGVSAPCKVTTEKLIDLWNESLQADETNKRFLEQRYDTRVIQRSLEEMESNEWLEKNSESCPCCGA<PI

Parental  QKLDGCNK-MTCTGCMQYFCWICMGFLSRANPYKHFTDPDSLCFNRLFHAVDVNGDIWEDEIED
          QK.DG.N..M.CTGCMQYFC.ICMGFLS.ANP..HF.DPDSLCFN.LFH..DVNGDIWEDEIED
Retrocopy QKFDGSNR<MMCTGCMQYFCGICMGFLSGANP*QHFPDPDSLCFNQLFHTMDVNGDIWEDEIED

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	63.30 RPM
SRP017611_kidney	0.00 RPM	97.10 RPM
SRP017611_liver	0.00 RPM	31.06 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_340 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Oryctolagus cuniculus	ENSOCUG00000016953	1 retrocopy	retro_ocun_340 ,