RetrogeneDB ID: retro_btau_902

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:20256130..20256460(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2V2
• Ensembl ID: ENSBTAG00000023218
• Aliases: UBE2V2, DDVIT1
• Description: Ubiquitin-conjugating enzyme E2 variant 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ43]

Sequence

>retro_btau_902
GGGGAGGGTTTGGTTAGCTGGGGCCTTGAAGCTGATGATGAATAAAGGACATGTTCAGGGTGGGTAACCATGGTGGTTCG
ATCACCAGGACAAATTATGAAAACGAAATATACAGACTTTAATTAGAATGTGAAACTAAATATCTAGAAGCATCTCCATT
GGTTATTTTTGTGACAGAATACTATATGAAATGAAATAAATAATGCCAGGGAAATGGTAGATGCACTGAGAATAGTGGTG
TTAGCTAAATGGCAAAATTCAGGAAACTTAAAAGTTATACTTCAAGAGTTAAGATACATAATACTGTTTAAAAATATAAA
GTCACCAGAA

Alignment

ORF - retro_btau_902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.64 %
• Parental protein coverage: 75.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GDGTVSWGLE-DDEDMTLTRWTGMIIGPP-RTNYENRIYSLKVECGPKYPEAPPSVRFVTKINM-NGINN
          G.G.VSWGLE.DDE..T...W..M....P.RTNYEN.IY.L..EC..KY.EA.P.V.FVT...M.N.INN
Retrocopy GEGLVSWGLEADDE*RTCSGWVTMVVRSP<RTNYENEIYRL*LECETKYLEASPLVIFVTEYYM>NEINN

Parental  SSGMVDARSIPVLAKWQNSYSIKVVLQELRRLMMSKENMKLPQ
          ...MVDA..I.VLAKWQNS...KV.LQELR.....K.N.K.P.
Retrocopy AREMVDALRIVVLAKWQNSGNLKVILQELRYIILFK-NIKSPE

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	16.08 RPM
ERP005899_muscle	0.00 RPM	12.67 RPM
SRP017611_brain	0.00 RPM	35.45 RPM
SRP017611_kidney	0.00 RPM	16.71 RPM
SRP017611_liver	0.00 RPM	8.08 RPM
SRP030211_testis	0.02 RPM	14.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_902 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_902 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_902 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2739
Sus scrofa	retro_sscr_524

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023218	1 retrocopy	retro_btau_902 ,
Bos taurus	ENSBTAG00000027316	4 retrocopies	retro_btau_1196, retro_btau_1226, retro_btau_1307, retro_btau_415,
Macropus eugenii	ENSMEUG00000016581	1 retrocopy	retro_meug_2093,
Monodelphis domestica	ENSMODG00000010191	10 retrocopies	retro_mdom_1065, retro_mdom_1151, retro_mdom_1167, retro_mdom_1435, retro_mdom_1660, retro_mdom_173, retro_mdom_1979, retro_mdom_736, retro_mdom_786, retro_mdom_979,
Oryctolagus cuniculus	ENSOCUG00000006933	1 retrocopy	retro_ocun_5,
Pongo abelii	ENSPPYG00000018575	1 retrocopy	retro_pabe_2739,
Ictidomys tridecemlineatus	ENSSTOG00000021769	2 retrocopies	retro_itri_568, retro_itri_900,