RetrogeneDB ID: retro_btau_1108

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:2899609..2900882(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000023971
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1108
ATGCACAGGAAACACCTCCAGGAGATACCTGACCAGAGTAGCAACGTTACCACCAGTTTCACGTGAGGATGGTATTCTAG
CAAGACTTCTGAACTGCTTTCAGGCACGGGGGTCTCCGCCCTGGAGAAGGAGGAGGTAGACAGTGAGAACATCCCCCAGG
AACTGCTTTCAAACCTGGGCCACCCACAAAGCCCCCCACGAAAACGGCTGAAAAGCAAAGGGAATGACAAGGACTTTGTG
ATTGTCCGCAGACCTAAGCTAAACCGAGAGAACTTTCCAGGTGTTTCTTGGGACTCCCTTCCAGACGAGCTGCTCTTAGG
AATCTTTTCCTTTCTGTGCCTCCCTGAACTCCTGAAAGTCTCCAGTGTTTGTAAGAGATGGTATCATCTAGCGTTTGACG
AGTCTCTCTGGCAAGACTGTAGACCTCGTGGGCAGAAACCTCTACCCAGATGTGGTTGGTCGGCTTTTGTCCCGAGGGGT
GGTTGCCTTCCGCTGTCCACGATCATTTATGGACCAACCGTCAGTTGATCATTTCAGCCCTTTCCGACTACAGCGCCTAG
ACCTGTCGAACTCTGTGATCTATGCGTCTACCCTGCACGGCCTTCTGTCTCACTGCTCCAAGTTGCAGAATCTCAGCCTG
GAAGGCCTCCGACTTTCAGATCCGGTTGTTGATAATCTTGCTCAGAACACAAATTTACCACGACTAAACCTTTCTGGGTG
TTCTGGATTCTCTGAATCTGCCCTGAAGACTTTGCTGAGCAACTGTTCCAGATTGGATGAACTGAACCTCTCTTGGTGCT
ATGATTTCACTGAAAAGCCTGTACAGGTGGCTGTTGCACATGTGTCAGAGACTATCACCCAGCTGAAGCTCAGCGGGTAC
CGAAAGAATCTGCAGAGATCAGATGTCTCTACCTTAGTTAGAAGATGTCCCAACCTTGTCCACCTAGACTTAAGTGATAG
TGTCATGCTGAAAAATGACTGCTTTCCAGAATTTTACCAACTCGATTACCTCCAACACCTATCACTCAGTCGGTGCTATG
ACATAATACCTGAAACTTTACTTGAACTTGGAGAAATTCCCACATTAAAAACACTACAAGTCTTTGGAATTGTACCAGAT
GGTACCCTTCAACTGTTAAAGGAAGCCCTCCCTCATCTACAGATTAATTGCTCCCATTTCACCACCATCGCCAGGCCAAC
CATTGGCAACAAGAAGAAGCAAGAGATATGGGGCATCAAATGCCTACTGTCACTGGAGAAGCCCAGTTGCCTA

Alignment

ORF - retro_btau_1108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRKHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPQELLSNLGHPQSPPRKRL
          MHRKHLQEIPDQSSNVTTSFT.GW.SSKTSELLSG.GVSALEKEEVDSENIPQELLSNLGHPQSPPRKRL
Retrocopy MHRKHLQEIPDQSSNVTTSFT*GWYSSKTSELLSGTGVSALEKEEVDSENIPQELLSNLGHPQSPPRKRL

Parental  KSKGNDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSSVCKRWYHLAFDESLWQ-T
          KSKGNDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFS.LCLPELLKVSSVCKRWYHLAFDESLWQ.T
Retrocopy KSKGNDKDFVIVRRPKLNRENFPGVSWDSLPDELLLGIFSFLCLPELLKVSSVCKRWYHLAFDESLWQ>T

Parental  VDLAGRNLYPDVVGRLLSRGVVAFRCPRSFMDQPLVEHFSPFRLQHLDLSNSVIDASTLHGLLSHCSKLQ
          VDL.GRNLYPDVVGRLLSRGVVAFRCPRSFMDQP.V.HFSPFRLQ.LDLSNSVI.ASTLHGLLSHCSKLQ
Retrocopy VDLVGRNLYPDVVGRLLSRGVVAFRCPRSFMDQPSVDHFSPFRLQRLDLSNSVIYASTLHGLLSHCSKLQ

Parental  NLSLEGLRLSDPVVDNLAQNTNLLRLNLSGCSGFSESALKTLLSSCSRLDELNLSWCYDFTEKHVQMAVA
          NLSLEGLRLSDPVVDNLAQNTNL.RLNLSGCSGFSESALKTLLS.CSRLDELNLSWCYDFTEK.VQ.AVA
Retrocopy NLSLEGLRLSDPVVDNLAQNTNLPRLNLSGCSGFSESALKTLLSNCSRLDELNLSWCYDFTEKPVQVAVA

Parental  HVSKTITQLNLSGYRKNLQRSDVSTLVGRCPNLVHLDLSDSVMLKNDCFPEFYQLNYLQHLSLSRCYDII
          HVS.TITQL.LSGYRKNLQRSDVSTLV.RCPNLVHLDLSDSVMLKNDCFPEFYQL.YLQHLSLSRCYDII
Retrocopy HVSETITQLKLSGYRKNLQRSDVSTLVRRCPNLVHLDLSDSVMLKNDCFPEFYQLDYLQHLSLSRCYDII

Parental  PETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKNQEIWGIKCRLSLE
          PETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKK.QEIWGIKC.LSLE
Retrocopy PETLLELGEIPTLKTLQVFGIVPDGTLQLLKEALPHLQINCSHFTTIARPTIGNKKKQEIWGIKCLLSLE

Parental  KPSCL
          KPSCL
Retrocopy KPSCL

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	1.95 RPM
ERP005899_muscle	0.11 RPM	8.34 RPM
SRP017611_brain	0.05 RPM	3.47 RPM
SRP017611_kidney	0.00 RPM	4.74 RPM
SRP017611_liver	0.00 RPM	0.91 RPM
SRP030211_testis	0.21 RPM	3.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1108 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1108 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,