RetrogeneDB ID: retro_btau_1229

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:66769029..66769748(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNFT1
• Ensembl ID: ENSBTAG00000009747
• Aliases: None
• Description: RING finger and transmembrane domain-containing protein 1 [Source:RefSeq peptide;Acc:NP_001069875]

Sequence

>retro_btau_1229
TGGGCCTCTAAATAATTTTCAAACCAGGCTTTTCTAAGAAAAATGTGCTCAAAATCCAGTAAGCTTAGTTACTGGTATTC
TTAGCAGGATTTTCCATTCTCTTTCATTCTTGGTCTCTTTATTACAACTTAATCTTTTTAAAATCCTATTTTGGATCATT
TGAACTTCTCAGAAGTACTTTGGATTATTGGAATTACAGACTTCATTTTGAAATTGCTTTTCATGGCTCAAAAAGTCTTA
TTATAGTGGTGCCTTCTTTCATCATGCTTTTTAAAGTCAAGGGTTCCTGGGATATGCTCTTAGAAGAATTAAGTCAGTTT
TACTGAATTTTATCCCCTACCAGTTTTGGTTTTATTACCTTATTTGCCTCAGGGAGTTTAACAGTATAATTAAATAGGTT
CTTTAGATATTAGTTGCTTTATTCTACCTCATTTTAAAGCTTTTGGATTTTTTGGAAATCTAAGAACTTTCAGATAGGTT
TGTGAATATTTTTTACACAACCAAGTTATGGAGTGACTTATTCAGATGTGGGTGATATTTGTTCAATATGTGAAGCTGAA
TTTCAGAAAAGTATTCTTCCCTTCTGTCAGCATATATTTTTTGAAGAGTGCATTACCTTATGGTTTTACAAAAAGAATGT
ATGTCCACTGCACAAGACTGTGATTTTAGACCATAGTCCCAAATGGAAAGATGGGGCTGTCTCATCACACCTTCAAATA

Alignment

ORF - retro_btau_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.11 %
• Parental protein coverage: 57.74 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  YANKSIVNQVFLRERCSK-IQCAWLLVFLAGSSVLLYYTFHSQSLYYSLIFL-NPTLDYSSFWEVLWVVG
          .A.K...NQ.FLR..CSK.IQ.A.LLVFLAG.S.L....FHS.SLYY.LIFL.NP.LD...F.EVLW..G
Retrocopy WASK*FSNQAFLRKMCSK<IQ*A*LLVFLAGFSIL----FHSWSLYYNLIFL>NPILDHLNFSEVLWIIG

Parental  ITDFILKFLFM-GLKCLILLVPSLIMPFKSKGYWYMLLEELCQYY-RTFVPIPVWFRYLISYGEFGNVTR
          ITDFILK.LFM.G.K.LI..VPS.IM.FK.KG.W.MLLEEL.Q.Y...F.P...WF.YLI...EF.....
Retrocopy ITDFILKLLFM<GSKSLIIVVPSFIMLFKVKGSWDMLLEELSQFY<LNFIPYQFWFYYLICLREFNSIIK

Parental  WSLGILLALLYLILKLLD-FFGHLRTFRQV-LRIFVTRPSYGVPASKRQCSDVDDICSICQAEFQKPILL
          ..L.IL.AL.YLILKLLD.FFG.LRTFR.V.L.IF.T.PSYGV..S.....D...IC....AEFQK.IL.
Retrocopy *VL*ILVALFYLILKLLD<FFGNLRTFR*V<L*IFFTQPSYGVTYS--DVGDICSIC---EAEFQKSILP

Parental  ICQHIFCEECITLWFNREKTCPLCRTVISDHINKWKDGATSSHLQI
          .CQHIF.EECITLWF.....CPL..TVI.DH..KWKDGA.SSHLQI
Retrocopy FCQHIFFEECITLWFYKKNVCPLHKTVILDHSPKWKDGAVSSHLQI

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	110.74 RPM
ERP005899_muscle	0.00 RPM	40.49 RPM
SRP017611_brain	0.00 RPM	9.46 RPM
SRP017611_kidney	0.30 RPM	55.24 RPM
SRP017611_liver	0.00 RPM	56.48 RPM
SRP030211_testis	0.00 RPM	50.69 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1229 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1229 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009747	2 retrocopies	retro_btau_1229 , retro_btau_413,
Cavia porcellus	ENSCPOG00000014736	1 retrocopy	retro_cpor_195,
Sus scrofa	ENSSSCG00000017671	2 retrocopies	retro_sscr_1201, retro_sscr_523,