RetrogeneDB ID: retro_btau_665

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 17:46486456..46487639(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCFD1
• Ensembl ID: ENSBTAG00000017565
• Aliases: None
• Description: sec1 family domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001178294]

Sequence

>retro_btau_665
AACTTTATTTCTGCCCTTTCAAGGAGTAAACTGGAATATATTGCAAATGTAGAAGTAGCAGCCATGCAGTTACTCAAGTA
TCCAGCTTTTGATCAGTATCTCAGTTTTATTACTTTGGAAAATGATATGCCTGTATGATACAATCAAAAATGAGGAAATG
TTTCATATTGTGCCATTAACAGTTCAGAAATCACAAATGCGGAAATGAAAACTGTTACGAACCGGAATGTTGACAGCCTC
TTCTGCTTTTCTGTTATGCTGGGTACTCTTCCTATAATCAGATAATTAGCAGGAACAGCAATGGAAATGAGAGCAGTGAA
AATAGATAAGAAGTTTCCGGAACATCTAAGAGATGCCAAAAAATGGTTTTACTACAGGTGATGCACTGGGAGCTGGCAGC
CTCAGCTTTCAAAGCCTTCTTCACTCCTGTTGACAGAAACATGGATCTGGCAACTCCTTTACATCATATTTGGACATATC
AATCCTACGCGTGTGATGTAGTGGATTTCCATGTACACAGAGTTAACCTGGAGGAATCTTCAGGAGTGAAAAAGTCCCTG
GCTGGTGCTAGTGTGACCTAGAGAAAAAACCAGGAAGTCGTATGATTTAACTCCAGTTGATACATTTTGGCAGAAACGTA
AAGGAAGTCCCTTCCCAGAGGTTTGGGAATCAGTTCAGCAAGAACTAGAATCTTAGAGCAGAGCACCAGAAGATGAGGTC
AAACGCCTGAGAAGTATGGGACCAGAAGGGAAAGATGAAGGGGCCACGAGGATGCTTCCTGACAACACTGCTCAGGTATC
CTCAGCTTTTGGTTCTTTGCCAGAAGACCTTGGAGAGGGGACAAAGACTTACTGATCTCCATAAAATGTTGCCACTGCTG
TCTTAGGACATGTAAAGGCATGAAAACTGGATGTATGTTTTGAATATAAAGAAAAAATAATGAGCAAAGCTTTCCTGGGC
AAATCTCTTCTAGAAGAAATATCAGACTCTGACGCAGGTAATCCAGGAGATAAATGAGGCATTTCTTATCTATCATGTAA
GTGCACAGCAAACAGCTTCTGAGGCTGATTTGGAGCCACACCAAAAAGCTGGAACTGACGCAGGATGCAACCTTAATTCC
TTACAATATATCAAACAGAGGAAGGCTTTTGCTAGGATGGCTTCAGCTCCTGCCATCTCAGGC

Alignment

ORF - retro_btau_665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.17 %
• Parental protein coverage: 61.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  NFISAISRSKLEDIANAALAASAVTQVAKVFDQYLNFITLEDDMFVLCNQNKELVSYRAINRPDITDTEM
          NFISA.SRSKLE.IAN...AA.........FDQYL.FITLE.DM.V..NQ....VSY.AIN...IT..EM
Retrocopy NFISALSRSKLEYIANVEVAAMQLLKYP-AFDQYLSFITLENDMPV*YNQK*GNVSYCAINSSEITNAEM

Parental  ETVMDTIVDSLFCFFVTLGAVPIIRCSRGTAAEMVAVKLDKKLRENLRDA-RNSLFTGDTLGAGQFSFQ-
          .TV....VDSLFCF.V.LG..PIIR...GTA.EM.AVK.DKK..E.LRDA..N...TGD.LGAG..SFQ.
Retrocopy KTVTNRNVDSLFCFSVMLGTLPIIR*LAGTAMEMRAVKIDKKFPEHLRDA>KNGFTTGDALGAGSLSFQ<

Parental  RPLLVL-IDRNIDLATPLHHTWTYQALVHDVLDFHLNRVNLEESSGMENSPAGARPK-RKN-KKSYDLTP
          .P...L..DRN.DLATPLHH.WTYQ....DV.DFH..RVNLEESSG...S.AGA....RKN..KSYDLTP
Retrocopy KPSSLL<VDRNMDLATPLHHIWTYQSYACDVVDFHVHRVNLEESSGVKKSLAGASVT*RKN>RKSYDLTP

Parental  VDKFWQKHKGSPFPEVAESVQQELES-YRAQEDEVKRLKSIMGLEGEDEGAISMLSDNTAKLTSAVSSLP
          VD.FWQK.KGSPFPEV.ESVQQELES..RA.EDEVKRL.S.MG.EG.DEGA..ML.DNTA...SA..SLP
Retrocopy VDTFWQKRKGSPFPEVWESVQQELES*SRAPEDEVKRLRS-MGPEGKDEGATRMLPDNTAQVSSAFGSLP

Parental  E-LLEK-KRLIDLHT-NVATAVLEHIKARKLDVYFEYEEKIMSKTTLDKSLLDIISDPDAGTPEDK-MRL
          E..LE...RL.DLH..NVATAVL.H.KA.KLDV.FEY.EKIMSK..L.KSLL..ISD.DAG.P.DK.MR.
Retrocopy E>TLERGQRLTDLHK<NVATAVLGHVKA*KLDVCFEYKEKIMSKAFLGKSLLEEISDSDAGNPGDK<MRH

Parental  F-LIYYISAQQAPSEADLEQYKKALTDAGCNLNPLQYIKQWKAFAKMASAPTSYG
          F.LIY..SAQQ..SEADLE...KA.TDAGCNLN.LQYIKQ.KAFA.MASAP...G
Retrocopy F<LIYHVSAQQTASEADLEPHQKAGTDAGCNLNSLQYIKQRKAFARMASAPAISG

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	33.81 RPM
ERP005899_muscle	0.00 RPM	38.48 RPM
SRP017611_brain	0.00 RPM	30.10 RPM
SRP017611_kidney	0.00 RPM	41.31 RPM
SRP017611_liver	0.00 RPM	33.07 RPM
SRP030211_testis	0.05 RPM	33.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_665 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_665 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_665 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017565	1 retrocopy	retro_btau_665 ,