RetrogeneDB ID: retro_btau_534

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:64603588..64604291(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000006725
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSBTAG00000013390
• Aliases: None
• Description: Proteasome subunit beta type-6 [Source:UniProtKB/Swiss-Prot;Acc:Q3MHN0]

Sequence

>retro_btau_534
ATGGCGGCCACCTTAGCAGCTGCTCGGGGAGAGGGGCCAGCACCAGTCTGGGGGCCCAAGGCCATTGCCTCTGACTGGGA
AAACCAGGAAGTCTCCACAGGGATCCCTATCATGGCTGTGCAATTTGATGGGGACATGATTCTAGAAGCCAACTCCAGAA
CAACCACGGAGTCATACACCACCAACCAAGTGACTGACAAGCTGACCCTTATTCATGGTGGTATTTTCTGTTGCCACTCA
GGCTCAGCAGCTGATCCTCAGGCAGAAGCCGATGCAGTCACTTATCAGCTTGGTTTGCACAGTGTTGAGCTGACTGAGCC
TCCACTGGACACACGGCAGCCAGCCTCCTTAAGGAGATGTGTTACCAATACCGAGAAGATCTGATGGCAGGAATCATCAC
TGAGGGCTGGGACTCCCAAGAAGGGGGACAGGTGTCCTCGGTACCCATGGAGGGTATGATGGTAAGGTAGGCCTTCACCA
TCGGGGACTCCGGGAGCTCTTATATCTATGGCTATGTTGAGGCTACCTACCGGGAAGGCATGACAAAGAATGTCTGCAAT
CCACTGCCAGTACTCTGTCTTTGGCCATGAAACAGGATGGTTCCAGCAGCAGAGTGATCCGCCTGGCAGCTATTGCAGAA
TCAGGGGTAGAATGGCAGGTTCTTCTGGGAGACGAGATTGTCCAATTCACTATTGCCACTTTA

Alignment

ORF - retro_btau_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.17 %
• Parental protein coverage: 98.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATLVAARGTRPAPAWGPEAIAPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTP
          MAATL.AARG..PAP.WGP.AIA.DWEN.EVSTG..IMAVQFDG...L.A.SRTTT.SY..N.VTDKLT.
Retrocopy MAATLAAARGEGPAPVWGPKAIASDWENQEVSTGIPIMAVQFDGDMILEANSRTTTESYTTNQVTDKLTL

Parental  IHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLV-HTAASLFKEMCYRYREDLMAGIIIAGWDP
          IH..IFCC.SGSAAD.QA.ADAVTYQLG.HS.EL.EPPL..HTAASL.KEMCY.YREDLMAGII..GWD.
Retrocopy IHGGIFCCHSGSAADPQAEADAVTYQLGLHSVELTEPPLD<HTAASLLKEMCYQYREDLMAGIITEGWDS

Parental  QEGGQVYSVPMGGMMVRQPFAIGGSGSS-YIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVI
          QEGGQV.SVPM.GMMVR..F.I.G...S...Y......Y..G....ECLQ.TA..L.LAM..DGSS..VI
Retrocopy QEGGQVSSVPMEGMMVR*AFTI-GDSGS<LLYLWLC*GYLPGRHDKECLQSTASTLSLAMKQDGSSSRVI

Parental  RLAAIAEPGVERQVLLGDQIPKFTIATL
          RLAAIAE.GVE.QVLLGD.I..FTIATL
Retrocopy RLAAIAESGVEWQVLLGDEIVQFTIATL

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	11.97 RPM
ERP005899_muscle	0.00 RPM	49.73 RPM
SRP017611_brain	0.00 RPM	26.08 RPM
SRP017611_kidney	0.00 RPM	39.42 RPM
SRP017611_liver	0.00 RPM	33.53 RPM
SRP030211_testis	0.01 RPM	29.97 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_534 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_534 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534 ,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807,