RetrogeneDB ID: retro_btau_1080

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 25:199095..199495(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX12
• Ensembl ID: ENSBTAG00000007871
• Aliases: None
• Description: sorting nexin-12 [Source:RefSeq peptide;Acc:NP_001096727]

Sequence

>retro_btau_1080
ATGTCAGACCTGGCAGTAGCTGACACCTGGAGCCTTAACTTGAAGCTGCAGGAACTGACCAACGCTTATAGGCTGCCAAG
TAACTTTCTGGATATCAACATCTTTAATCCACAGACGGTAGGCGTGGGCTGCACTCGCTTCACCCACCTACGAGATTTGC
ATGTAAACAAAACTACCTGTTTTCAAACTGAAGGAGTCCTGTGTATGACGGTGCTGCAGTAACTTTGAGTGACTAGAAAA
TGAGCTGGAGCAAGAGAGAACGATTGTATTAATAGTCCCACCACTGCCCGGGAAAGTCTTGAAATGGCAGCTCCCTTTTC
GAGGAAATGAAAGGGTCTTTGAGGAGTCCTTTATTGGAGAAAAGAGGTAGGGCCTCAAACAGTTTATTAGCAGAATTGCT

Alignment

ORF - retro_btau_1080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.66 %
• Parental protein coverage: 80.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSDTAVADTRRLNSKPQDLTDAYGPPSNFLEIDIFNPQTVGVGRARFT-TYEVRMRTNLPIFKLKESCVR
          MSD.AVADT..LN.K.Q.LT.AY..PSNFL.I.IFNPQTVGVG..RFT.TYE..M.T.LP.FKLKESCV.
Retrocopy MSDLAVADTWSLNLKLQELTNAYRLPSNFLDINIFNPQTVGVGCTRFT>TYEICM*TKLPVFKLKESCV*

Parental  RRYSDFEWLKNELERDSKIV--VPPLPGKALKRQLPFRGDEGIFEESFIEERRQGLEQFINKIA
          R..S.FE.L.NELE....IV..VPPLPGK.LK.QLPFRG.E..FEESFI.E.R.GL.QFI..IA
Retrocopy RCCSNFE*LENELEQERTIVLIVPPLPGKVLKWQLPFRGNERVFEESFIGEKR*GLKQFISRIA

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	11.97 RPM
ERP005899_muscle	0.00 RPM	63.45 RPM
SRP017611_brain	0.00 RPM	39.10 RPM
SRP017611_kidney	0.00 RPM	52.40 RPM
SRP017611_liver	0.00 RPM	17.06 RPM
SRP030211_testis	0.00 RPM	8.44 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1080 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1080 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080 ,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452,