RetrogeneDB ID: retro_ocun_1605

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018711:2707563..2707992(+)
• Located in intron of: ENSOCUG00000001833

Retrocopy information

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

Parental gene information

• Parental gene symbol: CWC15
• Ensembl ID: ENSOCUG00000001629
• Aliases: None
• Description: CWC15 spliceosome-associated protein homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26939]

Sequence

>retro_ocun_1605
ACAACCTCCTCTTCAGCAATAAAGAACCCTTGGCTAGGGCAGAGTCCTGATGCCATCTTCCCCACAGGGGAGCCTCTGGC
AGACGAGGAAGATGAAGGCTATGAAGAGGGGAGTGTTGATGACACAGCTGCTCTTCTTGAAGAACCGGAAAAAAATTATA
ATGAAAGAACAGGTGAACAGGCCAGGAAGGAATAGGAATTAAAAGCTGAAGAAGAGAGAAGATCTGTTTGGGAGACACTT
TGGGTGAATAACCTCTCCTTAATCTCACTGGCCCAGCCCAGCCTTAGCCAACTTCCAAAGTCACAGAAGGCAGGATGCTG
TGCTGTCTTTGAGAACTGCATGAAAGGCACAGGTGAGCAGGAGAAAGGTGCGTACACGATTCACTGAGGTTTGACTTTGC
GCAAAAGCTTCAGGGAGAAGTCCACGAAA

Alignment

ORF - retro_ocun_1605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.33 %
• Parental protein coverage: 63.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTSSSVSKKPRLDQIPAANLDADDPLTDEEDEDFEEESDDDDTAALLAELEKIKKERAEEQARKEQEQKA
          TTSSS..K.P.L.Q.P.A......PL.DEEDE..EE.S.DD.TAALL.E.EK...ER..EQARKE.E.KA
Retrocopy TTSSSAIKNPWLGQSPDAIFPTGEPLADEEDEGYEEGSVDD-TAALLEEPEKNYNERTGEQARKE*ELKA

Parental  -EEERIRMENILSGN-PLLNLTGPSQP-QANFKVKRRWDDDV-VFKNCAKGVDDQKKDKRFVNDTLRSEF
          .EE.R...E.....N.PLLNLTGP.QP..ANF...RR.D....VF.NC.KG...Q.K........L....
Retrocopy EEERRSVWETLWVNN<PLLNLTGPAQP<LANFQSHRRQDAVL<VFENCMKGTGEQEKGAYTIH*GL--TL

Parental  HKKFMEKYIK
          .K.F.EK..K
Retrocopy RKSFREKSTK

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	52.37 RPM
SRP017611_kidney	0.00 RPM	56.25 RPM
SRP017611_liver	0.00 RPM	12.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1605 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1605 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1605 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011392	1 retrocopy	retro_amel_1913,
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Dipodomys ordii	ENSDORG00000011075	1 retrocopy	retro_dord_313,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Oryctolagus cuniculus	ENSOCUG00000001629	4 retrocopies	retro_ocun_1037, retro_ocun_1605 , retro_ocun_679, retro_ocun_743,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,