RetrogeneDB ID: retro_btau_32

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 4:41064512..41066816(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047294
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CUL1
• Ensembl ID: ENSBTAG00000008736
• Aliases: None
• Description: cullin-1 [Source:RefSeq peptide;Acc:NP_001180162]

Sequence

>retro_btau_32
ATGTCATCGGACTGGAGCCAGAATCCCAGTGAACTGAATCATCTTGGCATTGACGAGCTCTGGGATAACATCAGAGCGGG
AATCCAGCAAGTGTATGCCAGACAAAGTATGGTGAAATCCAGATACATAGAACTCTACACTCTTCTTTATAACCACTGTT
TATATGTGTCCCCTCAAGCCCAGACTCAATCAAAAAAGGGGCAGAAGCTGAGGGAAGATAAGACTGTTGGCTTCGAATTA
TACAAACGAATTAAAGAATTTTTGAAGAATCACTTGACAAATCTTCCTAAGGATGGAGAAGATTTAATGGATATAGGAAT
ACTGAAGTTCTATACTCAACAATGGGAAGATTACCAGTTTTCGAGCAAAGTGCTGAATGGGATTTGTGCCCGCCTCAATA
AACATTTACTTAATAGCACAAATAACGAAGGACACAATGTTTGTGAAATATATTCTCTCGCAATGGTGACTTGGAGAGAT
TGTCTTTTCAGGCCATTGAATAAACAAGTAACAAATGCTGTTTTAAAACTGATTGAAAAGGAAAGAAATGGTGAATCCAT
CAATACAAGACTGATAAGTGGTGCTATCCAGTCTTACTTGGAACTGGGGGTGAATGAAGATAATCAGTTTGAGGAGAGCC
CTATGCTAACAGTGTACAAAGAAGCCTTTGAATCTCAGTTCTTGGCTGACACAGAGAGATATTATACCAGAAAGAGTACT
GAATTGTTGCAGCAGAACCCAGTTACTGAATATATGAAAAAGGTGGAGGCTCTTCTGCTGGAGGAGCGGCGGAGGGCCCG
GGTCTACCTTCACCAGAGCAGCAAGGGCAAGCTAGCCAGGAAATGCAGGCAGGTGCTCGTGGAGAAACACTTGGAGATTT
TCCTCACAGAATTCCAGAATTTACTGAACGCCAACAAAAGTGAAGATTTGGGTCGCATGTATAGGCTCATATATAGAATC
AAGAATGGCCTGGGAGAATTTAAAAAGATCCTGGAGACACACATTCATAATCAGGGTCTTTCAGCAATTGAGGAGTGTGG
AGAAGCTGCTTTAAATGACCCCAGAATGTATGTAGAGACAGTATTGAATATCCATAAAAAATACAATGCCCTGGTGATAT
CAGCATTCAGGAACCATGCTGACTTCGTGGCTGCACTGGACAAGGCATGCAGCGGCTTCATAAACAACAATGCAGTTACC
AAAATGGCTCAGTCATCCAGTAAATCCCCTGAGTTGCTGGCTCAATACTGTGATTCCTTGTTGAAGAAGAGTTCCAAGAA
CCCAGAAGAAGCAGAACTAGAAGACACACTTAACCACGTGATGACGGTCTTTAAGTATATGGATGACAAAGATGTGGTTC
AGAAGTTCTACACGAAAATGCTGGCCAAAAGGCTTGTCCATCAGAACAGTGCGAGTGACGATGCTGAAGCAAGCATGGTC
TCTAAGTTAAAGCAAGCTTGTGGTTTTGAGTATACCTCCAAACTTCAGCGGATGTTTCAAGACATTGGTGTAAGCAAAGC
TTTGAATGCGCAGTTCAAAAAGCACCTGATGGATTCAGAGCCTTTGGACTTAGATTTCAGTATTCACGTTCTGAGTTACG
GATGGTGGCCCTTTGAGGAATCTTGTACAGTTCTCTTGCCATCAGAGCTGGAACCATGTTATCGGCGCTTCACTGCATTT
TATGCCAGCTGTTACAGTGACAGAAAATTGTCATGGGCATATCAACTGTCTGAAGGAGAATTAGTAACAAACTACTTCAA
AAACAACTACACTTTGCGTGTATCTACATTTCAGATGGCCATCCTGCTCCAGTACAACACGGAAGATGCTTACACCATTC
AACAGCTGATGGACAGCACTCAGATCAAAATGGACATTGTGGCACAAGTCTTACAGATTTTATTGAAGTTTAAGTTACTG
GTTTTGGAAGACAAAAGTGCAAATGTTGACGAGGTGGAATTGAAGCCAGACACCTTAATAAAATTACATTTTGGTTATAA
AAGTAAGAAATTAAGGGTTAATATCAGCTTGCCAATGAAAATTGAACAGAAGCGGGAACAAGAAACCATGTACAAAAACA
TTGAGGAAGATCGCAAACTGCTGATCCAGGCGGCTATTGTGAGAATAATGAAAATGAGGAAGGTTGTAAAACACCAGCAG
TTACTCGGAGAAGTAGCGACTCAGTTGTCCTCAGTATTCAAGCCTCAGATCTCAGTGATTAAGAAATGTATTGACATTCT
GATCGAGAAAGAGTATTTGGAGCGAGTGGGTGATGAAAAGGACACCTACAGTTACCTGGCTTAA

Alignment

ORF - retro_btau_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.48 %
• Parental protein coverage: 91.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKSKKGQTPGGAQFVGLELYKRLKEFLKNYLTNLLKDGEDLMDESVLKFYTQQWEDYRFSSKVLNGICAY
          ..SKKGQ.......VG.ELYKR.KEFLKN.LTNL.KDGEDLMD...LKFYTQQWEDY.FSSKVLNGICA.
Retrocopy TQSKKGQKLREDKTVGFELYKRIKEFLKNHLTNLPKDGEDLMDIGILKFYTQQWEDYQFSSKVLNGICAR

Parental  LNRHWVRRECDEGRKGIYEIYSLALVTWRDCLFRPLNKQVTNAVLKLIEKERNGETINTRLISGVVQSYV
          LN.H.......EG.....EIYSLA.VTWRDCLFRPLNKQVTNAVLKLIEKERNGE.INTRLISG..QSY.
Retrocopy LNKHLLNSTNNEGHN-VCEIYSLAMVTWRDCLFRPLNKQVTNAVLKLIEKERNGESINTRLISGAIQSYL

Parental  ELGLNEDDAFAKGPTLTVYKESFESQFLADTERFYTRESTEFLQQNPVTEYMKKAEARLLEEQRRVQVYL
          ELG.NED..F...P.LTVYKE.FESQFLADTER.YTR.STE.LQQNPVTEYMKK.EA.LLEE.RR..VYL
Retrocopy ELGVNEDNQFEESPMLTVYKEAFESQFLADTERYYTRKSTELLQQNPVTEYMKKVEALLLEERRRARVYL

Parental  HESTQDELARKCEQVLIEKHLEIFHTEFQNLLDADKNEDLGRMYNLVSRIQDGLGELKKLLETHIHNQGL
          H.S....LARKC.QVL.EKHLEIF.TEFQNLL.A.K.EDLGRMY.L..RI..GLGE.KK.LETHIHNQGL
Retrocopy HQSSKGKLARKCRQVLVEKHLEIFLTEFQNLLNANKSEDLGRMYRLIYRIKNGLGEFKKILETHIHNQGL

Parental  AAIEKCGEAALNDPKMYVQTVLDVHKKYNALVMSAFNNDAGFVAALDKACGRFINNNAVTKMAQSSSKSP
          .AIE.CGEAALNDP.MYV.TVL..HKKYNALV.SAF.N.A.FVAALDKAC..FINNNAVTKMAQSSSKSP
Retrocopy SAIEECGEAALNDPRMYVETVLNIHKKYNALVISAFRNHADFVAALDKACSGFINNNAVTKMAQSSSKSP

Parental  ELLARYCDSLLKKSSKNPEEAELEDTLNQVMVVFKYIEDKDVFQKFYAKMLAKRLVHQNSASDDAEASMI
          ELLA.YCDSLLKKSSKNPEEAELEDTLN.VM.VFKY..DKDV.QKFY.KMLAKRLVHQNSASDDAEASM.
Retrocopy ELLAQYCDSLLKKSSKNPEEAELEDTLNHVMTVFKYMDDKDVVQKFYTKMLAKRLVHQNSASDDAEASMV

Parental  SKLKQACGFEYTSKLQRMFQDIGVSKDLNEQFKKHLTNSEPLDLDFSIQVLSSGSWPFQQSCTFALPSEL
          SKLKQACGFEYTSKLQRMFQDIGVSK.LN.QFKKHL..SEPLDLDFSI.VLS.G.WPF..SCT..LPSEL
Retrocopy SKLKQACGFEYTSKLQRMFQDIGVSKALNAQFKKHLMDSEPLDLDFSIHVLSYGWWPFEESCTVLLPSEL

Parental  ERSYQRFTAFYASRHSGRKLTWLYQLSKGELVTNCFKNRYTLQASTFQMAILLQYNTEDAYAVQQLTDST
          E..Y.RFTAFYAS..S.RKL.W.YQLS.GELVTN.FKN.YTL..STFQMAILLQYNTEDAY..QQL.DST
Retrocopy EPCYRRFTAFYASCYSDRKLSWAYQLSEGELVTNYFKNNYTLRVSTFQMAILLQYNTEDAYTIQQLMDST

Parental  QIKMDILAQVLQILLKSKLLVLEDENANVDEVELKPDTLIKLYLGYKNKKLRVNINVPMKTEQKQEQETT
          QIKMDI.AQVLQILLK.KLLVLED..ANVDEVELKPDTLIKL..GYK.KKLRVNI..PMK.EQK.EQET.
Retrocopy QIKMDIVAQVLQILLKFKLLVLEDKSANVDEVELKPDTLIKLHFGYKSKKLRVNISLPMKIEQKREQETM

Parental  HKNIEEDRKLLIQAAIVRIMKMRKVLKHQQLLGEVLTQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEK
          .KNIEEDRKLLIQAAIVRIMKMRKV.KHQQLLGEV.TQLSS.FKP...VIKKCIDILIEKEYLERV..EK
Retrocopy YKNIEEDRKLLIQAAIVRIMKMRKVVKHQQLLGEVATQLSSVFKPQISVIKKCIDILIEKEYLERVGDEK

Parental  DTYSYLA
          DTYSYLA
Retrocopy DTYSYLA

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	21.27 RPM
ERP005899_muscle	0.00 RPM	28.14 RPM
SRP017611_brain	0.00 RPM	69.75 RPM
SRP017611_kidney	0.00 RPM	44.45 RPM
SRP017611_liver	0.00 RPM	21.37 RPM
SRP030211_testis	0.01 RPM	430.68 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_32 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_32 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008736	1 retrocopy	retro_btau_32 ,
Myotis lucifugus	ENSMLUG00000002479	1 retrocopy	retro_mluc_349,
Otolemur garnettii	ENSOGAG00000014715	1 retrocopy	retro_ogar_3491,