RetrogeneDB ID: retro_btau_541

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:33087317..33088046(+)
• Located in intron of: ENSBTAG00000000620

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUCKS1
• Ensembl ID: ENSBTAG00000008001
• Aliases: None
• Description: Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 [Source:UniProtKB/Swiss-Prot;Acc:Q29S11]

Sequence

>retro_btau_541
ATGTCTTGGCCTGTCAGAAATAGGAAGGTCGTTGATTATTCACAATTTTAGGAATCCGATGATGCTGATGAAGATTATGG
AAGAGATTCAGGCCCTCCAGCTAAGAAAATTCGATCATCTCCCCGAGAAGCTAAAAATAAGAGGCGATCTGGAAAGAATT
CACAGGAAGATAGTGAGGACTCGGAAGAAAAAGATGTGAAGACTAAGAAGGATGATTCTCATTCAGCAGAGGACAGTGAA
GATGAAAAAGAAGATCATAAAAATGTGTGCCAGCAAGGGCAGGCAGCCTCTAAAGCAGCCTCTAAACAGAGGGAGATGCT
CATGGAAGATGTGGGCAGTGAGGAGGAGCAAGAAGAGGAGGACGAGGCGCCATTCCAGGAGAAAGATTCCGGCAGTGATG
AGGATTTCCTAGTAGAAGATGATGATGATAGTGACTCTGGCAGTTCAAAAAAGAAAAACAAAAAGATGGTTAAGAAGTCG
AAGCCTGAGAGAAAAGAAAAGAAAATGCCGAAGTCCAGGCTAAAGGCCACAGTGACGCCAAGTCCTGTGAAAGGCAAGGG
GAAAGTGGGTCGCCCCACAGCTTCAAAGGCATCAAAGGAAAAGACTCCTTCTCCCAAAGAAGAAGATAAGGAACCAGAAA
GCCCTCTGGAAAAGAAAATGTCTTCAAGCCCTCCACTTGAGAAATCTGGGGATGAAGGTTCTGAAGATGAAGCCCAATCT
GGGGAAGAT

Alignment

ORF - retro_btau_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRPVRNRKVVDYSQFQESDDADEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKK
          MS.PVRNRKVVDYSQF.ESDDADEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKK
Retrocopy MSWPVRNRKVVDYSQF*ESDDADEDYGRDSGPPAKKIRSSPREAKNKRRSGKNSQEDSEDSEEKDVKTKK

Parental  DDSHSAEDSEDEKEDHKNVRQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLVED
          DDSHSAEDSEDEKEDHKNV.QQ.QAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLVED
Retrocopy DDSHSAEDSEDEKEDHKNVCQQGQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEKDSGSDEDFLVED

Parental  DDDSDYGSSKKKNKKMVKKSKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKEEDE
          DDDSD.GS.......MVKKSKPERKEKKMPK.RLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKEED.
Retrocopy DDDSDSGSXXXXXXXMVKKSKPERKEKKMPKSRLKATVTPSPVKGKGKVGRPTASKASKEKTPSPKEEDK

Parental  EPESPLEKKASSSPPPEKSGDEGSEDDAQSGED
          EPESPLEKK.SSSPP.EKSGDEGSED.AQSGED
Retrocopy EPESPLEKKMSSSPPLEKSGDEGSEDEAQSGED

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	95.82 RPM
ERP005899_muscle	0.48 RPM	78.55 RPM
SRP017611_brain	0.37 RPM	118.45 RPM
SRP017611_kidney	0.53 RPM	129.21 RPM
SRP017611_liver	0.08 RPM	66.98 RPM
SRP030211_testis	0.15 RPM	33.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_541 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541 ,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,