RetrogeneDB ID: retro_ocun_1247

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:88703165..88703512(+)
• Located in intron of: ENSOCUG00000008270

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCK
• Ensembl ID: ENSOCUG00000001265
• Aliases: None
• Description: deoxycytidine kinase [Source:HGNC Symbol;Acc:2704]

Sequence

>retro_ocun_1247
TTTTAAAGATCCATGTATAGTGATAGGTGTATTTTTGCATCTAAATTATATGAATTTGACTGCATGAATGAAACAATAGA
CAGCTATCAAGACTGCCATGACTGGATGAATAACCAGTTTGTCCACAGCCTCGAATTGGGTGGAATCATTTTGAGCTACT
CTAGAAAAATACTGAATAGAATATATTTTCAGGGAAGAAATGAAGAGCAAGGCATTTCTCTGAATATTTAGAGAAGTTTC
ATTATGAACATGAATGCTGACTCTTGGAAAGAACACTGAAAACTAACTTCGATGATCTACGTGAAGTGCCTGTCTTAACG
TTAGATGGTAATGAGGACTTTAAAGAA

Alignment

ORF - retro_ocun_1247 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 50.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FERSVYSDRYIFASNLYESDCMNETEWTIYQDWHDWMNNQFGQNLELDGIIYLRATPEKCLNRIYLRGRN
          F.RS.YSDR.IFAS.LYE.DCMNET....YQD.HDWMNNQF...LEL.GII.......K.LNRIY..GRN
Retrocopy F*RSMYSDRCIFASKLYEFDCMNETIDS-YQDCHDWMNNQFVHSLELGGIIL--SYSRKILNRIYFQGRN

Parental  EEQGIPL-EYLEKLHYKHESWLLHRTLKTNFDYLQEVPILTLDVNEDFKD
          EEQGI.L.EYLEK.HY.HE..LL.RTLKTNFD.L.EVP.LTLD.NEDFK.
Retrocopy EEQGISL<EYLEKFHYEHEC*LLERTLKTNFDDLREVPVLTLDGNEDFKE

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	0.06 RPM	27.15 RPM
SRP017611_kidney	0.10 RPM	5.98 RPM
SRP017611_liver	0.46 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1247 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1247 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1247 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247 ,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9,