RetrogeneDB ID: retro_btau_1119

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 27:3761027..3761573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OTUB1
• Ensembl ID: ENSBTAG00000003967
• Aliases: None
• Description: ubiquitin thioesterase OTUB1 [Source:RefSeq peptide;Acc:NP_001029891]

Sequence

>retro_btau_1119
ATTCAGCAAGAGATCACTGTGCAGAACCCGCTGGTCTGGGTCCTACACAGATAGTGCACTGAGGATAACAACGTCTGTCA
ACAGAAGGTCAAGGACCGCCACAGAAAGTACTCCTACATCCGCAAGACCAGGGCTGGTGGAAACTGCCTCTATCGCGCTT
TTGGATTCTCCCACTTGGAGGCGTTGCTGGATGACAGCAAGGAATCGCAGCGGTTCAAGGCTGTGTCTGCCAAGAGTGAA
GAGGACCTGGTGTCCCAGGGCTTCCCTGAGCTCACAACTGAGGATTTCCACCACACGTTCATGGGCCTGAACGAGCGGGT
GGAGACGCAGACCTCAGTGGCCAACCTGCTGGTCTCCTTCAGTGACCAGAGTACCTTGGACCACCTGGTGATCTACCTGC
GGCTGCTTCCCTCGGGCGACCTGCAGCGGAACAGCAAGTTCTTGGAGCACTGCATCCAGGGTGGGCGGACCATCAGGGAA
CTCTGCCAGCAGGAGGTGGAGCCCGCGCCGAAGGGGGGCGGCCACATCCTCATCCTGGCTCTGGCT

Alignment

ORF - retro_btau_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.03 %
• Parental protein coverage: 67.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQNPLVSERLELSVLYKEYAEDDNIYQQKIKDLHKKYSYIRKTRPDGNCFYRAFGFSHLEALLDDSKELQ
          .Q...........VL.....ED.N..QQK.KD.H.KYSYIRKTR..GNC.YRAFGFSHLEALLDDSKE.Q
Retrocopy IQQEITVQNPLVWVLHR*CTEDNNVCQQKVKDRHRKYSYIRKTRAGGNCLYRAFGFSHLEALLDDSKESQ

Parental  RFKAVSAKSKEDLVSQGFTEFTIEDFHNTFMDLIEQVEKRTPVADLLASFNDQSTSDYLVVYLRLLTSGY
          RFKAVSAKS.EDLVSQGF.E.T.EDFH.TFM.L.E.VE..T.VA.LL.SF.DQST.D.LV.YLRLL.SG.
Retrocopy RFKAVSAKSEEDLVSQGFPELTTEDFHHTFMGLNERVETQTSVANLLVSFSDQSTLDHLVIYLRLLPSGD

Parental  LQRESKFFEHFIEGGRTVKEFCQQEVEPMCKESDHIHIIALA
          LQR.SKF.EH.I.GGRT..E.CQQEVEP..K...HI.I.ALA
Retrocopy LQRNSKFLEHCIQGGRTIRELCQQEVEPAPKGGGHILILALA

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	9.30 RPM
ERP005899_muscle	0.00 RPM	54.95 RPM
SRP017611_brain	0.00 RPM	53.86 RPM
SRP017611_kidney	0.00 RPM	35.92 RPM
SRP017611_liver	0.00 RPM	17.82 RPM
SRP030211_testis	0.07 RPM	116.55 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1119 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1119 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1119 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018084	1 retrocopy	retro_amel_1270,
Bos taurus	ENSBTAG00000003967	1 retrocopy	retro_btau_1119 ,
Canis familiaris	ENSCAFG00000014729	2 retrocopies	retro_cfam_1376, retro_cfam_2023,
Equus caballus	ENSECAG00000002621	1 retrocopy	retro_ecab_760,
Myotis lucifugus	ENSMLUG00000012235	2 retrocopies	retro_mluc_1257, retro_mluc_614,
Mustela putorius furo	ENSMPUG00000013314	1 retrocopy	retro_mputfur_1057,
Pteropus vampyrus	ENSPVAG00000017099	2 retrocopies	retro_pvam_131, retro_pvam_274,
Rattus norvegicus	ENSRNOG00000021175	1 retrocopy	retro_rnor_2431,
Sarcophilus harrisii	ENSSHAG00000004156	1 retrocopy	retro_shar_87,