RetrogeneDB ID: retro_ocun_500

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:44020227..44021193(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022088
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSNK1A1
• Ensembl ID: ENSOCUG00000006669
• Aliases: CSNK1A1, CKIALPHA
• Description: casein kinase 1, alpha 1 (CSNK1A1), mRNA [Source:RefSeq mRNA;Acc:NM_001082373]

Sequence

>retro_ocun_500
ATGGCGAGCAGCAGCGACTCCAGGGCCAAACTAATTGTCGGAGGGAAATATAAACTGGTCCGGAAGATCGGGTCTGGGTC
CTTTGGGGACATTTATCTGGCGATTAACATCACCAACGGCGAGGAAGTGGCAGTGAAGCTAGAATCTCTGAAGGCCAAGC
ATTCCCAGTTGCTGTACGAGAGCAAAGTCTATAAGATTCTTCAGGGTGGGGTCGGCATCCCGCACATACGGTGGTATGGT
CCGGAGAAAGACCATAATGCCTTGGTCTTGGATCTTCTGGGACCCAGCCTCCAGGACCTCTTCAGTTTCTGTTCAAGGAA
GTTCACAATGAAAACTGTCCTTATGTTGGCTGACCAGATGATCAGCAGAATTGAATATGTGCATACAAAGAATTTTATAC
ACAGAGACATTAAACCAGATAACTTCCTCATGGGCATTGGACGGCACTGTAATAAGTTATTCCTTATTGATTTTGGTTTG
GCCAAAAAGTACCGAGACAACAGGACCAGGCAACACATACCGTACAGAGAAAATAAGAGCTTCACTGGCACTGCGCGGTA
TGCCAGCATCAATGCGCATCTCGGTATTGAGCAGAGTCGCCGGGATGACATGGAAGCATTAGGATACGTTTTGATGTATT
TTAATAGAACCAGCCTGCCATGGCAAGGACTGAAGGCTGCAACAAAGAAACAAAAATATGAAAAGATTAGTGAAAAGAAG
ATGTCCACTCCTGTGGAAATTTTATGTAAGGGGTTTCCTGCAGAGTTTTCCATGTATTTAAACTATTGTCGTGGGCTGCG
CTTTGAAGAAGTCCCTGATTACATGTATCTGAGGCAGCTCTTCCGCATCCTTTTCAGGACCCTGAACCACCAATATGACT
ACACATTTGATTGGACAATGTTGAAGCAGAAGGTAGCATAGCAAGTAGTCTCTTCCAGTGGGCAGGTTCAGCAGACCCAC
GGCCCC

Alignment

ORF - retro_ocun_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.68 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSSGSKAEFIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESQKARHPQLLYESKLYKILQGG
          MASSS.S.A..IVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLES.KA.H.QLLYESK.YKILQGG
Retrocopy MASSSDSRAKLIVGGKYKLVRKIGSGSFGDIYLAINITNGEEVAVKLESLKAKHSQLLYESKVYKILQGG

Parental  VGIPHIRWYGQEKDYNVLVMDLLGPSLEDLFNFCSRRFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
          VGIPHIRWYG.EKD.N.LV.DLLGPSL.DLF.FCSR.FTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD
Retrocopy VGIPHIRWYGPEKDHNALVLDLLGPSLQDLFSFCSRKFTMKTVLMLADQMISRIEYVHTKNFIHRDIKPD

Parental  NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYREDKNLTGTARYASINAHLGIEQSRRDDMESLGYV
          NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYRE.K..TGTARYASINAHLGIEQSRRDDME.LGYV
Retrocopy NFLMGIGRHCNKLFLIDFGLAKKYRDNRTRQHIPYRENKSFTGTARYASINAHLGIEQSRRDDMEALGYV

Parental  LMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEVLCKGFPAEFAMYLNYCRGLRFEEAPDYMYLRQL
          LMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVE.LCKGFPAEF.MYLNYCRGLRFEE.PDYMYLRQL
Retrocopy LMYFNRTSLPWQGLKAATKKQKYEKISEKKMSTPVEILCKGFPAEFSMYLNYCRGLRFEEVPDYMYLRQL

Parental  FRILFRTLNHQYDYTFDWTMLKQKAAQQAASSSGQGQQAQTP
          FRILFRTLNHQYDYTFDWTMLKQK.A.Q..SSSGQ.QQ...P
Retrocopy FRILFRTLNHQYDYTFDWTMLKQKVA*QVVSSSGQVQQTHGP

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	165.73 RPM
SRP017611_kidney	0.00 RPM	128.72 RPM
SRP017611_liver	0.00 RPM	57.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_500 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_500 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_500 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005326	2 retrocopies	retro_btau_1662, retro_btau_49,
Canis familiaris	ENSCAFG00000018286	1 retrocopy	retro_cfam_1887,
Callithrix jacchus	ENSCJAG00000021121	1 retrocopy	retro_cjac_2680,
Homo sapiens	ENSG00000113712	1 retrocopy	retro_hsap_32,
Gorilla gorilla	ENSGGOG00000013926	3 retrocopies	retro_ggor_1178, retro_ggor_742, retro_ggor_984,
Myotis lucifugus	ENSMLUG00000002910	4 retrocopies	retro_mluc_1531, retro_mluc_2134, retro_mluc_2215, retro_mluc_597,
Macaca mulatta	ENSMMUG00000001758	2 retrocopies	retro_mmul_2207, retro_mmul_295,
Monodelphis domestica	ENSMODG00000009937	1 retrocopy	retro_mdom_2005,
Oryctolagus cuniculus	ENSOCUG00000006669	7 retrocopies	retro_ocun_1068, retro_ocun_1098, retro_ocun_1506, retro_ocun_500 , retro_ocun_502, retro_ocun_506, retro_ocun_644,
Sorex araneus	ENSSARG00000011446	1 retrocopy	retro_sara_518,
Sarcophilus harrisii	ENSSHAG00000015356	1 retrocopy	retro_shar_834,
Sus scrofa	ENSSSCG00000014435	1 retrocopy	retro_sscr_560,
Ictidomys tridecemlineatus	ENSSTOG00000022141	1 retrocopy	retro_itri_1378,
Drosophila melanogaster	FBgn0015024	4 retrocopies	retro_dmel_10, retro_dmel_32, retro_dmel_40, retro_dmel_67,