RetrogeneDB ID: retro_btau_525

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 13:40950548..40951324(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSBTAG00000013562
• Aliases: None
• Description: S-phase kinase-associated protein 2 [Source:RefSeq peptide;Acc:NP_001095522]

Sequence

>retro_btau_525
AGGAAACATTTCCAGGAGACACCCAACCAGAGGACCAATGCCACCACCAGTTTCACGTGGGGATGGGGGTTCTAGACTTC
TGACTGTTTTCAGGCATGGGGGTCTCCACCCTGGAGAAGGAGGAGATGGACAGTGAGACTATCCCCCAGCAACTGCTTTC
AAACCTGGGCCACCCACAGAGTCCCCCATGAAAATGGCTGAAAAGCAAAGGAAATGACAAGGACTTTGAGATTATCCGCA
GACCTAAGCTAAACAAGAGAACTTTCCAGCTATTTCTTGGGACTCCCTTCCAGACGAGCTACTCTTAGGAATCTTTTCCT
GTCTGTGCCTCCCTGAACTCCTGAAAGTCTCCAGTGTTTGTTAAAAGACAGCATTATCTAGAGTTTGATGAGTCTCTCTG
GCAGACTGTGGACCTCACGGGCAGAAACCTCTACCCAGATGTGGTTGGTCGGCTTCTGTCCTGATGGGTAGTTGCCTTCT
GCTGCCCGTGATCATTTATGGACCAATTGTTAGTTGAATATTTCAGCCCTTTTTGTCTACAGCACCTGGACCTATCGAAC
TTAGTGATTGACGTGTTTACCCTCCACGGCCTTCTGTCTCACTGCTCCAAGTTGCAGAATCTCAGCCTGGAAGGCCTCCG
GCTTTCTGATCCCATTGTTGATAATCTTGCTAAGAAAACAAATTTACTGCAACTCAACCTTTCTGGGCATTCTGGATTCT
CTGAATCTGCCCTGAAGATTTTGCTGAGCAGCTGTTCCAGATTGGATGAGCTGAGC

Alignment

ORF - retro_btau_525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.23 %
• Parental protein coverage: 61.32 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMG-VSALEKEEVDSENIPQELLSNLGHPQSPPRKRLK
          RKH.QE.P.Q..N.TTSFTWGW....TS......G.VS.LEKEE.DSE.IPQ.LLSNLGHPQSPP.K.LK
Retrocopy RKHFQETPNQRTNATTSFTWGW-GF*TSDCFQAWG<VSTLEKEEMDSETIPQQLLSNLGHPQSPP*KWLK

Parental  SKGNDKDFVIVRRPKLNR-ENFPGVSWDSLPDELLLGIFSCLCLPELLKVSSVC-KRWYHLAFDESLWQT
          SKGNDKDF.I.RRPKLN..ENFP..SWDSLPDELLLGIFSCLCLPELLKVSSVC.KR...L.FDESLWQT
Retrocopy SKGNDKDFEIIRRPKLNK<ENFPAISWDSLPDELLLGIFSCLCLPELLKVSSVC>KRQHYLEFDESLWQT

Parental  VDLAGRNLYPDVVGRLLSRGVVAFRCPRSFMDQPLVEHFSPFRLQHLDLSNSVIDASTLHGLLSHCSKLQ
          VDL.GRNLYPDVVGRLLS..VVAF.CP.SFMDQ.LVE.FSPF.LQHLDLSN.VID..TLHGLLSHCSKLQ
Retrocopy VDLTGRNLYPDVVGRLLS*WVVAFCCP*SFMDQLLVEYFSPFCLQHLDLSNLVIDVFTLHGLLSHCSKLQ

Parental  NLSLEGLRLSDPVVDNLAQNTNLLRLNLSGCSGFSESALKTLLSSCSRLDELN
          NLSLEGLRLSDP.VDNLA..TNLL.LNLSG.SGFSESALK.LLSSCSRLDEL.
Retrocopy NLSLEGLRLSDPIVDNLAKKTNLLQLNLSGHSGFSESALKILLSSCSRLDELS

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	0.07 RPM	1.95 RPM
ERP005899_muscle	0.00 RPM	8.34 RPM
SRP017611_brain	0.00 RPM	3.47 RPM
SRP017611_kidney	0.00 RPM	4.74 RPM
SRP017611_liver	0.00 RPM	0.91 RPM
SRP030211_testis	0.02 RPM	3.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_525 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_525 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525 , retro_btau_555,
Choloepus hoffmanni	ENSCHOG00000006980	1 retrocopy	retro_chof_1604,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,
Tupaia belangeri	ENSTBEG00000016814	1 retrocopy	retro_tbel_4354,