RetrogeneDB ID: retro_btau_1734

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:31022582..31023044(+)
• Located in intron of: ENSBTAG00000034045

Retrocopy information

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

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_1734
ACCCAGGCAGTAGCTGATGGAGTCACTTAATCAGCTTGGTTTCCACAGCATTGAGCTGAATGAGCCTCTGCTGGTATACA
CGGCAGCCAGCCTCTTTAAGGAAATGTGTTATTGATACCAAGAAGACCTGATGGCAGAAATCATCACTGCTGGCTGGAAC
CCCCAAGAAGGGGGCAGGTGTACTCAGTGCCTATGGGGAGTATGATAGTACAACAGTCCTTTGCCACTGGGGGCTCCAGG
AGCTCCTATTTCTTTGGCTGTGTCAATGCTACCTACTGGGAAGGCATGACCAAGGAAGAATGCCTGCAGTTTACTGCCAG
TGCTTTCACTTTGGACATGGAGCAGGATGGTTCCAGTGGAGGGGTTATCCACCTGGCAGCCATTGAGGAATCAGGGGTAG
AGTGGCAGGTACTTCTTCGAGACCAGAGTCCCAAATTCACCAATGCCACTTTACCACCTCTC

Alignment

ORF - retro_btau_1734 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TQAVADAVT-YQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGG-QVYSVPMGGM
          TQAVAD.VT..QLGFHSIELNEP.LV.TAASLFKEMCY.Y.EDLMA.II.AGW.PQEGG.QVYSVPMG.M
Retrocopy TQAVADGVT>NQLGFHSIELNEPLLVYTAASLFKEMCY*YQEDLMAEIITAGWNPQEGG<QVYSVPMGSM

Parental  MVRQPFAIGGSGSSYIYGYVDATYREGMTKEECLQFTANALALAMERDGSSGGVIRLAAIAEPGVERQVL
          .V.Q.FA.GGS.SSY..G.V.ATY.EGMTKEECLQFTA.A..L.ME.DGSSGGVI.LAAI.E.GVE.QVL
Retrocopy IVQQSFATGGSRSSYFFGCVNATYWEGMTKEECLQFTASAFTLDMEQDGSSGGVIHLAAIEESGVEWQVL

Parental  LGDQIPKFTIATLPPL
          L.DQ.PKFT.ATLPPL
Retrocopy LRDQSPKFTNATLPPL

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_1734 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1734 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1734 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,