RetrogeneDB ID: retro_btau_123

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:64998394..65000221(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000019143
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPN1
• Ensembl ID: ENSBTAG00000005191
• Aliases: None
• Description: dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 precursor [Source:RefSeq peptide;Acc:NP_001076074]

Sequence

>retro_btau_123
ATGGAGGCGCCCGCAGTCCACCTGCTGCCGTTGCTGCTGCTGTTTGCGGCCTGGGCCCCGGAGCCAGGCAGCACCTCTGC
GGAGGCTCTGCCTCTGGTCAACGAAGAGGTGAGGCGCACGGTGGACCTGAGCAGCCACCTGGCCAAGGTGACAGCCGAGG
TGGTCCTGGCTCACACGGGCAGTGACTCCTCGCCCCGCGCTGCCTCCTTCCTGGTAGCGCTGGAGCCTGAGTTCGAGGCC
CAGCTGGCACACCTCGGCGTGCAGGTGACGGGAGTGGATGAGGAAGCCAACAGTCTGGAAGTACAGGAGACCAAAATTAA
CGGTAAAAGCGGGAGATTCTTCACAGTCCAACTCCCAGTTGCTCTTGATCCTGGGGCCGAGGTTTCAGTCGTTGTGGAAG
CCGTTTATACCCACGCGATTCAGCCGTATCCAATCCAGATCACCCAGTCTCAGAAACAGTTTGTGGTGTTTGAGGGGAAC
CATTATTTTTACTCTCCCTACCCGACCAAGACGCAAACCATGCATGTGAAGCTCGCCTCCCCAAACGTGGAGAGCTATAC
CAAATTGGGCAACCCCATGCGCCACGAGAATCTCCTGGATTACGGCCCTTTCCACGACATCCCTGCCTATAGTCAGGATA
GTTTTAAAGTACATTCTGAGAACAACAGCCCTTTCCTGACCGTCACCAGCATGACCCGAGTCATCGAGGTCTCCCACTGG
GGTAATATTGCTGTGGAAGAAAACGTGAACCTGAAGCACACGGGGGCTGTGCTGAAGGGGTCTTTTTCGCGTTATGATTA
TGACAAATGGATAGATAGTGGCATCTCCTCCATCCGTTCTTTTAAGACCATCCTTCCTGCCTCTGCCCAGGATGTTTATT
ACCGGGATGAGATTGGCAGCATTTACACCAGACACCTCCTTATTTTGGATGACTCGGTGGAGATGGAAATGAAGCCTCGT
TTCCCTCTCTTTGGCGGGTGGAAGACTCATTACATCATTGGCTACAACCTCCCAAGCTATGAGTACCTCTATAATTTGGG
AGACCAGTATGTGTTGAAAATGAGGCTTGTGGACCACGTGTTTGATAAACAAGTGATAGACTCTCTGACTGTGAAGATCA
TCCTCCCTGAAGGAGCCAGGAACATCCAGGTGGACAGTCCCTATGAGATCAGCCGAGCCCCCGACAAGCTATACTATACC
TACCTGGACACATTTGGCCGCCCTGTGATCGTGGCCCACAAGAAAAACCTGGTGGAACAGCATATTCAGGACATCATGGT
GCACTACACCTTCAGCAAGGTGCTCATGCTACAGGAGCCCCTGCTGTTGGTGGCCACCTTCTCCATTCTGTTCTTCACCG
TCGTCATCTATGTCAGGCTGGATTTATCCATCACAAAGGATCCAGCTGCAGAAGCCAGGATGAAGGTGGCTTGCATAATA
GAGCAGGTCTTGACCCTGGTCAGCAAGAGACTAGGTCTCTACCATCACTTTAACAAGACAGTCAATAGATACAAACAGTC
CCGGGATGTGTCCGTCCTCAACAGTGGCAAGAAGAGCCTGGAGATGGAGCACAAGGCTTTGACCAGCGAGGTGGCACTGC
TGCAGGCCAGGCTGAAGACCGAGGGCTCCAACCTGTGTGACAAAGTGAGCGAAATGCAAAAACTGGACACGCAGGTCAAG
CAGCTGGTCCTGAAGTCAGCAGTGGAGGCCGAGTGGCTGGTGGCCGGCAAGCTCAAGAAAGACATGTACATCCAGAATAA
GAAGCTCATTTCAGGAAAGCGACAGGAGCTGGTCAGCAAGATTGAACACATCCTGGATACCCTGTAG

Alignment

ORF - retro_btau_123 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAPAARLLPPLLLLLSACAPAPGRASSDAPPLVNEDVKRTVDLSSHLAKVTAEVVLAHAGSGSSPRAAS
          MEAPA..LLP.LLLL..A.AP.PG..S..A.PLVNE.V.RTVDLSSHLAKVTAEVVLAH.GS.SSPRAAS
Retrocopy MEAPAVHLLP-LLLLFAAWAPEPGSTSAEALPLVNEEVRRTVDLSSHLAKVTAEVVLAHTGSDSSPRAAS

Parental  FLLALEPELEARLAHLGVQVKGEDEEENNLEVRETSIKGQSGRFFTVKLPVALDPGAKISVIVEAVYTHV
          FL.ALEPE.EA.LAHLGVQV.G.DEE.N.LEV.ET.I.G.SGRFFTV.LPVALDPGA..SV.VEAVYTH.
Retrocopy FLVALEPEFEAQLAHLGVQVTGVDEEANSLEVQETKINGKSGRFFTVQLPVALDPGAEVSVVVEAVYTHA

Parental  LQPYPTQITQSEKQFVVFEGNHYFYSPYPTKTQTMRVKLASRNVESYTKLGNPTRSEDLLDYGPFRDIPA
          .QPYP.QITQS.KQFVVFEGNHYFYSPYPTKTQTM.VKLAS.NVESYTKLGNP.R.E.LLDYGPF.DIPA
Retrocopy IQPYPIQITQSQKQFVVFEGNHYFYSPYPTKTQTMHVKLASPNVESYTKLGNPMRHENLLDYGPFHDIPA

Parental  YSQDTFKVHSENNSPFLTITSMTRVIEVSHWGNIAVEENVDLKHTGAVLKGPFSRYDYQRQPDSGVSSVR
          YSQD.FKVHSENNSPFLT.TSMTRVIEVSHWGNIAVEENV.LKHTGAVLKG.FSRYDY....DSG.SS.R
Retrocopy YSQDSFKVHSENNSPFLTVTSMTRVIEVSHWGNIAVEENVNLKHTGAVLKGSFSRYDYDKWIDSGISSIR

Parental  SFKTILPAAAQDVYYRDEIGNVSTSHLLILDDSVEMEIRPRFPLFGGWKTHYIVGYNLPSYEYLYNLGDQ
          SFKTILPA.AQDVYYRDEIG...T.HLLILDDSVEME..PRFPLFGGWKTHYI.GYNLPSYEYLYNLGDQ
Retrocopy SFKTILPASAQDVYYRDEIGSIYTRHLLILDDSVEMEMKPRFPLFGGWKTHYIIGYNLPSYEYLYNLGDQ

Parental  YALKMRLVDHVFDEQVIDSLTVKIILPEGAKNIQVDSPYEISRGPDELHYTYLDTFGRPVIVAHKENLVE
          Y.LKMRLVDHVFD.QVIDSLTVKIILPEGA.NIQVDSPYEISR.PD.L.YTYLDTFGRPVIVAHK.NLVE
Retrocopy YVLKMRLVDHVFDKQVIDSLTVKIILPEGARNIQVDSPYEISRAPDKLYYTYLDTFGRPVIVAHKKNLVE

Parental  QHIQDIVVHYTFNKVLMLQEPLLVVATFYILFFTVIVYVRLDFSITKDPAAEARMKVACITEQVLTLVNK
          QHIQDI.VHYTF.KVLMLQEPLL.VATF.ILFFTV..YVRLD.SITKDPAAEARMKVACI.EQVLTLV.K
Retrocopy QHIQDIMVHYTFSKVLMLQEPLLLVATFSILFFTVVIYVRLDLSITKDPAAEARMKVACIIEQVLTLVSK

Parental  RLGLYRHFDETVNRYKQSRDVSTLNSGKKSLETEHKALTSGLALLQSRLKTEGSDLCDKVSEMQRLDAQV
          RLGLY.HF..TVNRYKQSRDVS.LNSGKKSLE.EHKALTS..ALLQ.RLKTEGS.LCDKVSEMQ.LD.QV
Retrocopy RLGLYHHFNKTVNRYKQSRDVSVLNSGKKSLEMEHKALTSEVALLQARLKTEGSNLCDKVSEMQKLDTQV

Parental  KELVLKAAVEAERLVAGKLKKDTYIENEKLISGKRQELVGKIDHILDAL
          K.LVLK.AVEAE.LVAGKLKKD.YI.N.KLISGKRQELV.KI.HILD.L
Retrocopy KQLVLKSAVEAEWLVAGKLKKDMYIQNKKLISGKRQELVSKIEHILDTL

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	53.50 RPM
ERP005899_muscle	0.00 RPM	376.12 RPM
SRP017611_brain	0.00 RPM	91.13 RPM
SRP017611_kidney	0.00 RPM	162.46 RPM
SRP017611_liver	0.00 RPM	368.41 RPM
SRP030211_testis	206.44 RPM	277.21 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_123 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_123 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_123 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005191	1 retrocopy	retro_btau_123 ,
Callithrix jacchus	ENSCJAG00000017529	1 retrocopy	retro_cjac_601,
Myotis lucifugus	ENSMLUG00000017213	1 retrocopy	retro_mluc_721,
Oryctolagus cuniculus	ENSOCUG00000011098	1 retrocopy	retro_ocun_899,