RetrogeneDB ID: retro_btau_885

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:99538459..99538845(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2B
• Ensembl ID: ENSBTAG00000008837
• Aliases: CSNK2B, CSKN2B
• Description: Casein kinase II subunit beta [Source:UniProtKB/Swiss-Prot;Acc:P67868]

Sequence

>retro_btau_885
CAATACATCCTCATCAGCTGTGGCATTGCCCAGATGTTGGAAGAGTACCAACAGGAAGACTTTGGCTACGGAGCCTGTGT
GTACTGTGGAAACCAACCAATGCTTCCCAGTGGCTTTTCAGACATCCCAAGTGAGGCCATGGTAAGCTCTACTGCCTCAA
ATGCTTGGATGTGTACACACATAAGTCACTGAGGCACCAACACATGGATGGCGTCTACTTTGGCACTGGTTTCCCTCACA
TGCTCTTCATGGTACACCCAAGTACTGGACAGAGGGCCACCAACCAGATTGTGTCCAGGCTCTATGGTTTCAAGATCCAT
TCAGTGGTCTACCAGCAGCAGCTCCAAGCCACCAGCAACTTCAAGAGCCCTGTTAGGATGGTTCGC

Alignment

ORF - retro_btau_885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.99 %
• Parental protein coverage: 60.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMV-KLYCPKCMDVYTPKSSRHHHT
          .YIL...GIAQMLE.YQQ.DFGY...VYC.NQPMLP.G.SDIP.EAMV.KLYC.KC.DVYT.KS.RH.H.
Retrocopy QYILISCGIAQMLEEYQQEDFGYGACVYCGNQPMLPSGFSDIPSEAMV<KLYCLKCLDVYTHKSLRHQHM

Parental  DGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIHPMAYQLQLQAASNFKSPVKTIR
          DG.YFGTGFPHMLFMVHP.....R..NQ.V.RLYGFKIH...YQ.QLQA.SNFKSPV...R
Retrocopy DGVYFGTGFPHMLFMVHPS-TGQRATNQIVSRLYGFKIHSVVYQQQLQATSNFKSPVRMVR

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
ERP005899_liver	0.00 RPM	27.97 RPM
ERP005899_muscle	0.00 RPM	81.56 RPM
SRP017611_brain	0.00 RPM	48.15 RPM
SRP017611_kidney	0.00 RPM	57.97 RPM
SRP017611_liver	0.00 RPM	42.28 RPM
SRP030211_testis	0.00 RPM	150.88 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_885 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_885 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,