RetrogeneDB ID: retro_ocun_815

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:97043627..97045128(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000007852
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UGP2
• Ensembl ID: ENSOCUG00000002137
• Aliases: None
• Description: UDP-glucose pyrophosphorylase 2 [Source:HGNC Symbol;Acc:12527]

Sequence

>retro_ocun_815
AAGGAAGATCTTAGCAAAGCAATGTCTCAAGAAGGTGCTTCTCAGTTCCAAGAAGTCATTCGACAAGAGCTAGAGTTATC
AGTGAAGAAGGAACTAGAAAAAATACTCACAACAGCACCAGCACAGGAGTTTGAGCACAGTAAAAAAAGATCTTGATGGA
TTTTGGAATAGATTTTGGCAAGAAAAGGGACCTTCTGTGGATTGGGGAAAAATTCAGAGACCTCCAGAAGATTCGATTCA
ACCCTATGAAAAGATAAAAGCTAGAGGCTTGCCTGATAATATACCTTCTGTGTTGAACAAACTGGTGGTGGTAAAACTCA
ATGGTGGTTTGGGAACCAGCATGGGTTGCAAAGGCCCTAAAAGTCTGATTGGCGTGAGGAATGAGAATACCTTTTTGGAT
CTGACTGTTCAGCAAATTGAACATTTGAACAAAACCTATAATACAGACGTTCCTCTTGTTTTAATGAACTCTTTTAACAC
AGATGAAGATACGAAAAAAATACTACAGAAGTATAATCGTCGTGTGAAAATCTACACTTTCAATCAAAGCAGGTACCCAA
GGATTAATAAAGAATCTTTACTTCCTGTGGCAAAAGATGTATCTTATTCAGGGGAAAATACAGAAGCTTGGTACCCACCA
GGTCATGGTGATATATACGCCAGTTTCTACAACTCTGGTTTGCTGGATACCTTTATAGGAGAAAGCAAAGAGTATATTTT
TGTGTCTAACATAGATAATCTGGGTGCCACAGTGGATCTTTATATTCTTAATCATCTAATGAATTCACCCAATGGAAAAT
GCTGTGAATTTGTCATGGAAGTCACAAATAAAACTCGTGCAGATGTAAAGGGTGGGACACTCACTCAGTATGAAGGCAAA
CTGAGACTGGTGGAAATCGCTCAAGTGCCAAAAGCACATGTTGATGAGTTCAAGTCTGTATCAAAATTCAAAATATTTAA
TACAAACAACCTATGGATTTCTCTTGCAGCAGTTAAAAGACTGCAGGAGCAGAATGCCATTGACATGGAAATCATTGTGA
ATCCAAAGACTTTGGATGGAGGCCTGAATGTCATTCAGTTAGAAACTGCAGTAGGAGCTGCCATTAAAAGTTTTGAGAAT
TCTCTAGGTATTAATGTTCCAAGGAGCCGTTTTCTGCCTGTCAAAACCACGTCAGATCTTTTGCTTGTGATGTCAAACCT
CTATAGCCTTAATGCAGGATCTTTGACAATGAGTGAAAAACGGGAATTTCCTACAGTGCCCTTGGTTAAATTAGGCAGTT
CTTTTACAAAGGTTCAAGATTATCTACGAAGATTTGAAAGTATACCAGATATGCTTGAATTGGATCACCTCACCATTTCA
GGAGATGTGACATTTGGCAAGAATGTGTCATTAAAGGGAACGGTTATCATCATTGCAAACCACGGTGACAGAATTGACAT
CCCACCTGGAGCAGTATTAGAGAACAAAATTGTATCTGGAAACCTTCGCATCTTGGACCAC

Alignment

ORF - retro_ocun_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.83 %
• Parental protein coverage: 97.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KSDLSKAMSQDGASQFQEVIRQELELSVKKELEKILTTAPAQEFEHTKK-DLDGFRKLFHRFLQEKGPSV
          K.DLSKAMSQ.GASQFQEVIRQELELSVKKELEKILTTAPAQEFEH.KK.DLDGF.....RF.QEKGPSV
Retrocopy KEDLSKAMSQEGASQFQEVIRQELELSVKKELEKILTTAPAQEFEHSKK>DLDGF---WNRFWQEKGPSV

Parental  DWGKIQRPPEDSIQPYEKIKARGLPDNISSVLNKLVVVKLNGGLGTSMGCKGPKSLIGVRNENTFLDLTV
          DWGKIQRPPEDSIQPYEKIKARGLPDNI.SVLNKLVVVKLNGGLGTSMGCKGPKSLIGVRNENTFLDLTV
Retrocopy DWGKIQRPPEDSIQPYEKIKARGLPDNIPSVLNKLVVVKLNGGLGTSMGCKGPKSLIGVRNENTFLDLTV

Parental  QQIEHLNKTYNTDVPLVLMNSFNTDEDTKKILQKYNHCRVKIYTFNQSRYPRINKESLLPVAKDVSYSGE
          QQIEHLNKTYNTDVPLVLMNSFNTDEDTKKILQKYN..RVKIYTFNQSRYPRINKESLLPVAKDVSYSGE
Retrocopy QQIEHLNKTYNTDVPLVLMNSFNTDEDTKKILQKYNR-RVKIYTFNQSRYPRINKESLLPVAKDVSYSGE

Parental  NTEAWYPPGHGDIYASFYNSGLLDTFIGEGKEYIFVSNIDNLGATVDLYILNHLMNSPNGKRCEFVMEVT
          NTEAWYPPGHGDIYASFYNSGLLDTFIGE.KEYIFVSNIDNLGATVDLYILNHLMNSPNGK.CEFVMEVT
Retrocopy NTEAWYPPGHGDIYASFYNSGLLDTFIGESKEYIFVSNIDNLGATVDLYILNHLMNSPNGKCCEFVMEVT

Parental  NKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNTNNLWISLAAVKRLQEQNAIDMEII
          NKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNTNNLWISLAAVKRLQEQNAIDMEII
Retrocopy NKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNTNNLWISLAAVKRLQEQNAIDMEII

Parental  VNPKTLDGGLNVIQLETAVGAAIKSFENSLGINVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKRE
          VNPKTLDGGLNVIQLETAVGAAIKSFENSLGINVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKRE
Retrocopy VNPKTLDGGLNVIQLETAVGAAIKSFENSLGINVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKRE

Parental  FPTVPLVKLGSSFTKVQDYLRRFESIPDMLELDHLTVSGDVTFGKNVSLKGTVIIIANHGDRIDIPPGAV
          FPTVPLVKLGSSFTKVQDYLRRFESIPDMLELDHLT.SGDVTFGKNVSLKGTVIIIANHGDRIDIPPGAV
Retrocopy FPTVPLVKLGSSFTKVQDYLRRFESIPDMLELDHLTISGDVTFGKNVSLKGTVIIIANHGDRIDIPPGAV

Parental  LENKIVSGNLRILDH
          LENKIVSGNLRILDH
Retrocopy LENKIVSGNLRILDH

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
SRP017611_brain	2.48 RPM	62.86 RPM
SRP017611_kidney	4.87 RPM	94.87 RPM
SRP017611_liver	4.78 RPM	225.06 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_815 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_815 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_815 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006960	1 retrocopy	retro_cjac_1709,
Cavia porcellus	ENSCPOG00000008459	1 retrocopy	retro_cpor_811,
Microcebus murinus	ENSMICG00000006509	1 retrocopy	retro_mmur_1277,
Oryctolagus cuniculus	ENSOCUG00000002137	1 retrocopy	retro_ocun_815 ,
Tursiops truncatus	ENSTTRG00000000694	1 retrocopy	retro_ttru_56,