RetrogeneDB ID: retro_btau_983

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:59556380..59557088(+)
• 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_983
GGGTTCTCTTTCGCTAAGTGTCACAGAAAGGCCATCTCAGAAGTCAATTTTGCAAAGATAAAGGACAAACTTCCAACAGC
CCAGAAAACCGGGACAACCACTGCGGGGGCGGTCTATGAGGATGGCGTGGTTTTCGCAAGAGATACGAGGGCGAGTAAAG
GGATGATTGCTGTTGACAAGAACTGTCAAAAACACACTTCATATCTCCTAACAGCTACTGCCGTGGTCCTGGGACCGCTG
TGGGCACAGACAAGACGACCTAGCTCATTTCCTCCAACCTGGAGCTCCACTCCCTTCGCCCGGGCTGCCTTCCCAGAGCT
GTGGCGGCCAGTCAGAGGTGGCCGCAGACAGATGCTTTCCGGGCAGCAAGGTTACACTGGGGCAGCCCTGGCTCTGGGGA
CGAGAGGTACTGGACCTCACCTCTGCAGCGTCTGTTCTCATGGTCAGCCGGCGAGCTGCCTTATGTCACCTTGGGTTCCG
GCTCCTTGACAGCCATGGCCATGTTTGAAGATGAATTCAGGACAGATATGGAGGAGGAGCAAGCCGAGAGGCTGGTGAGT
GAAGCCACAGCAGCTGACGCCCTCATGACTTGGGGTCTGGAAGTGACACTGGTCTCGCTGTCACCAGCAAGAGCGAGCTG
GATCCTCTGCACCGCACTCAGTGCCCCAAAGGAAGGGAGGGGTGGGCCAGCACAGGGGCGAGGGGGGC

Alignment

ORF - retro_btau_983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.07 %
• Parental protein coverage: 85.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GFSFDNCRRNAVLEADFAKKGYKLPTARKTGTTIAGVVYKDGIVLGADTRATEGMVVADKNC-SKIHFIS
          GFSF..C.R.A..E..FAK...KLPTA.KTGTT.AG.VY.DG.V...DTRA..GM...DKNC.SK.HFIS
Retrocopy GFSFAKCHRKAISEVNFAKIKDKLPTAQKTGTTTAGAVYEDGVVFARDTRASKGMIAVDKNC<SKTHFIS

Parental  PNIYCCGAGTAADTDMTTQLISSNLELHSLSTGRLPRVVTANRMLKQM-LFR-YQGYIGAALVLGGVDVT
          PN.YC.G.GTA..TD.TT.LISSNLELHSL..G.LPR.V.A.....Q...FR..QGY.GAAL.L.G...T
Retrocopy PNSYCRGPGTAVGTDKTT*LISSNLELHSLRPGCLPRAVAASQRWPQTDAFR>QQGYTGAALAL-GTRGT

Parental  GPHLYSIYPHG-STDKLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKKLVSEAIAAGIF-NDLGSGSNID
          GPHL.S...HG.S...LPYVT.GSGSL.AMA.FED.FR.DMEEE.A..LVSEA.AA.....DLGSGS...
Retrocopy GPHLCSVCSHG<SAGELPYVTLGSGSLTAMAMFEDEFRTDMEEEQAERLVSEATAADAL<HDLGSGSDTG

Parental  LCVISKSKLDFLR-PYSVPNKKGTRFGRYRCEKG
          L.V.SKS.LD.L..P.SVP..KG...G..R.E.G
Retrocopy LAVTSKSELDPLH<PHSVPQRKG-GVGQHRGEGG

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	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	0.08 RPM	66.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_983 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_983 has 0 orthologous retrocopies within eutheria group .

---

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,