RetrogeneDB ID: retro_ocun_362

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:51762722..51763056(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2B
• Ensembl ID: ENSOCUG00000023483
• Aliases: CSNK2B, CK-II, CK2N, Phosvitin
• Description: casein kinase 2, beta polypeptide (CSNK2B), mRNA [Source:RefSeq mRNA;Acc:NM_001160283]

Sequence

>retro_ocun_362
TCAGAGGAAATGTCCCAGATTTCCCGGTTCTAAGGGCTACACAGAAATGAATTATTCTGTAAAATGACCAAGAGTACATC
CAGGACAAATGCAATCTTACTAGATTGAATGAGCATGTTCCTCCCTAGTGACAAGTTCCAGACAGGATTTTGAACCCAGA
ACCTGATGAACAGCAGAAAGATAATCCCAACCAGAGCAACCTTATTGAGAAAGATGAAAGCTTTTACGGGTTAGCCGATA
CCCTCTCGTTGTTATCCATCTTGGCATCACCCAGATGTCAGAGTAGTGGCAGCGAGACTTTGGCTAATGTCCCTAGGTGT
ATTGTGAGAACCAG

Alignment

ORF - retro_ocun_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.9 %
• Parental protein coverage: 53.02 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEEVSWISWFCGLRGNEFFCEV-DEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLI
          SEE.S.IS.F.GL..NE.FC...D..YIQDK.NLT.LNE.VP...Q..D.IL..EPDE...DNPNQS.LI
Retrocopy SEEMSQISRF*GLHRNELFCKM<DQEYIQDKCNLTRLNEHVPP**QVPDRILNPEPDEQQKDNPNQSNLI

Parental  EQAAEMLYGLIHARYILT-NRGIAQMLEKYQQGDFGYCPRVYCENQ
          E...E..YGL......L....GI.QM.E..Q..DFG.CP.VYCENQ
Retrocopy EK-DESFYGLADTLSLLS<HLGITQMSE*WQR-DFG*CP*VYCENQ

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	91.23 RPM
SRP017611_kidney	0.00 RPM	96.39 RPM
SRP017611_liver	0.00 RPM	37.07 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_362 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_362 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_362 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005751	1 retrocopy	retro_acar_107,
Bos taurus	ENSBTAG00000008837	1 retrocopy	retro_btau_885,
Callithrix jacchus	ENSCJAG00000002996	1 retrocopy	retro_cjac_2700,
Dasypus novemcinctus	ENSDNOG00000018728	1 retrocopy	retro_dnov_697,
Dipodomys ordii	ENSDORG00000014179	1 retrocopy	retro_dord_45,
Erinaceus europaeus	ENSEEUG00000006417	2 retrocopies	retro_eeur_331, retro_eeur_555,
Echinops telfairi	ENSETEG00000015168	3 retrocopies	retro_etel_225, retro_etel_271, retro_etel_769,
Felis catus	ENSFCAG00000007642	2 retrocopies	retro_fcat_1749, retro_fcat_206,
Macropus eugenii	ENSMEUG00000004095	10 retrocopies	retro_meug_1158, retro_meug_1316, retro_meug_1598, retro_meug_187, retro_meug_1939, retro_meug_40, retro_meug_525, retro_meug_528, retro_meug_751, retro_meug_752,
Monodelphis domestica	ENSMODG00000015287	4 retrocopies	retro_mdom_1433, retro_mdom_1558, retro_mdom_704, retro_mdom_936,
Mustela putorius furo	ENSMPUG00000011129	1 retrocopy	retro_mputfur_154,
Oryctolagus cuniculus	ENSOCUG00000023483	2 retrocopies	retro_ocun_1477, retro_ocun_362 ,
Ochotona princeps	ENSOPRG00000012138	1 retrocopy	retro_opri_970,
Sarcophilus harrisii	ENSSHAG00000001478	2 retrocopies	retro_shar_672, retro_shar_693,
Sus scrofa	ENSSSCG00000001414	1 retrocopy	retro_sscr_538,
Tursiops truncatus	ENSTTRG00000014103	2 retrocopies	retro_ttru_1595, retro_ttru_1740,