RetrogeneDB ID: retro_btau_1722

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: GJ059756.1:1207..1884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.56882
• Ensembl ID: ENSBTAG00000003067
• Aliases: None
• Description: proteasome subunit beta type-7 precursor [Source:RefSeq peptide;Acc:NP_001033616]

Sequence

>retro_btau_1722
GGGTTCTCTTTCGCTAAGTGTCACAGAAAGGCCATCTCAGAAGTCAAGTTTGCAAAGATGAAGGACAAACTTCCAACAGC
CCGGGAAACCGGGACAACCACTGCGGGGCGGTCTGTGAGGATGGCGTGGTTTTCGCAAGAGATACGAGGGCGAGTAAAGG
GATGATTGCTGTTGACAAGAACTGTCAAAAATACACTTCATATCTCCTAACAGCTACTGCCGTGGTCCTGGGACCGCTGT
GGGCACAGACAAGACGACCTAGCTCATTTCCTCCAACCTGGAGCTCCACTCCCTTCGCCCGGGCTGCCTTCCCAGAGCTG
TGACGGCCGGTCAGAGGCGGCCGCAGACACATGCTTTCCGGGCAGCAAGGTTACACTGGGGCAGCCCTGGCTCTGGGGAC
GAGAGGTACTGGACCTCACCTCTACAGCGTGTGTTCTCATGGTCAGCCGTCGAGCTGCCTTATGTCACCTTGGGTTCCGG
CTCCTTGACAGCCATGGCCATGTTTGAAGATGAATTCAGGACAGATATGGAGGAGGAGCAAGCCGAGAGGCTGGTGAGTG
AAGCCACAGCAGCTGACGCCCTCATGACTTGGGGTCTGGAAGTGACACTGGTCTCACTGTCACCAGCAAGAGCGAGCTGG
ATCCTCTGCACCGCAGTCAGTGCCCCAAAGGAAGGGA

Alignment

ORF - retro_btau_1722 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.82 %
• Parental protein coverage: 81.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  GFSFDNCRRNAVLEADFAKKGYKLPTARKTGTTIAG-VVYKDGIVLGADTRATEGMVVADKNC-SKIHFI
          GFSF..C.R.A..E..FAK...KLPTAR.TGTT.AG..V..DG.V...DTRA..GM...DKNC.SKIHFI
Retrocopy GFSFAKCHRKAISEVKFAKMKDKLPTARETGTTTAG<AVCEDGVVFARDTRASKGMIAVDKNC<SKIHFI

Parental  SPNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQM-LFR-YQGYIGAALVLGGVDV
          SPN.YC.G.GTA..TD.TT.LISSNLELHSL..G.LPR.VTA.....Q...FR..QGY.GAAL.L.G...
Retrocopy SPNSYCRGPGTAVGTDKTT*LISSNLELHSLRPGCLPRAVTAGQRRPQTHAFR>QQGYTGAALAL-GTRG

Parental  TGPHLYSIYPHG-STDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKKLVSEAIAAGIF-NDLGSGSNI
          TGPHLYS...HG.S...LPYVT.GSGSL.AMA.FED.FR.DMEEE.A..LVSEA.AA.....DLGSGS..
Retrocopy TGPHLYSVCSHG<SAVELPYVTLGSGSLTAMAMFEDEFRTDMEEEQAERLVSEATAADAL<HDLGSGSDT

Parental  DLCVISKSKLDFLR-PYSVPNKKG
          .L.V.SKS.LD.L..P.SVP..KG
Retrocopy GLTVTSKSELDPLH<PQSVPQRKG

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	0.07 RPM	29.49 RPM
ERP005899_muscle	0.00 RPM	75.17 RPM
SRP017611_brain	0.00 RPM	44.67 RPM
SRP017611_kidney	0.00 RPM	54.53 RPM
SRP017611_liver	0.00 RPM	46.82 RPM
SRP030211_testis	0.09 RPM	66.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1722 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1722 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003067	2 retrocopies	retro_btau_1722 , retro_btau_983,
Echinops telfairi	ENSETEG00000005432	2 retrocopies	retro_etel_2093, retro_etel_231,
Homo sapiens	ENSG00000136930	1 retrocopy	retro_hsap_1303,
Gorilla gorilla	ENSGGOG00000012164	1 retrocopy	retro_ggor_1019,
Nomascus leucogenys	ENSNLEG00000017268	1 retrocopy	retro_nleu_2947,
Otolemur garnettii	ENSOGAG00000003513	1 retrocopy	retro_ogar_2828,
Pongo abelii	ENSPPYG00000019596	1 retrocopy	retro_pabe_1092,
Pan troglodytes	ENSPTRG00000021354	1 retrocopy	retro_ptro_893,
Pteropus vampyrus	ENSPVAG00000000204	2 retrocopies	retro_pvam_1271, retro_pvam_866,
Rattus norvegicus	ENSRNOG00000011732	3 retrocopies	retro_rnor_1581, retro_rnor_1582, retro_rnor_2469,
Sorex araneus	ENSSARG00000009395	1 retrocopy	retro_sara_532,
Tupaia belangeri	ENSTBEG00000009196	2 retrocopies	retro_tbel_2889, retro_tbel_751,