RetrogeneDB ID: retro_rnor_2277

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:27665905..27667468(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000031342
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uap1
• Ensembl ID: ENSRNOG00000002926
• Aliases: Uap1, RGD1561967
• Description: UDP-N-acetylhexosamine pyrophosphorylase [Source:RefSeq peptide;Acc:NP_001178859]

Sequence

>retro_rnor_2277
AATGTTAATGACCTCAGACAGAGGTTGTCCGCGGCTGGGCAGCAGCACCTGCTGCAGTTCTGGAATGAGCTGTCAGAAGC
CCAGCAGGGAGAACTTTATATGGAACTCCAAGCCATGAACTTTGAAGAGCCGAACTCATTTTTCCAGAAGGCCGTTGGCG
AATTTGATCGATCTTCTCACCAAGAAAAGGTGGATGCACGGATGGAGCCTGTGCCCAGACAGGTTTTGGGCAGTGCTACC
AGAGATCAAGACCAGCTGCAGGCCTGGGAGAGCCAAGGACTTTCCCAGATTTCTCAGAACAAAGTAGCAGTTCTTCTTCT
AGCTGGTGGGCAGGGGTCAAGTCTTGGAGTCACGTATCCCAAGGGCATGTATGATGTGGGCTTGCCATCCCACAAGACAC
TTTTCCAGATACAAGCAGAACGTATTCTGAAGCTGCAGCAGTTAGCTGAGAAACAGTATGGCAACAAGTGTATCATCCCC
TGGTATATAATGGCCAGTGGCAGAACGATGGAATCGATGAAGGAGTTCTTTACAAAGCACAAGTTCTTTGGTTTAAAAAA
GGAGAACGTGGTCTTTTTCCAGCAGGGAATGCTGCCTGCTATGAGCTTTGATGGGAAAGTTATCTTGGAAGAGAAAAACA
AAGTCTCTATGGCTCCAGATGGGAATGGTGGTCTCTACCGGGCTCTTGCAGCCCAAAACATTGTGGAGGACATGGAGCAA
AGAGGCATCTGGAGTATTCATGTCTATTGTGTGGATAACATACTGGTGAAAGTGGCAGACCCTCGGTTCATTGGATTCTG
CATTCAGAAAGGAGCAGACTGTGGGGCAAAGGTGGTAGAGAAAACCAACCCCACGGAGCCAGTCGGCGTGGTTTGCCGGG
TGGATGGGGTGTACCAGGTAGTGGAGTACAGTGAGATCTCTCTGGCCACAGCTCAGAAGCGGAGCTCAGACGGAGGGCTG
CAGTTCAATGCGGGGAACATCGCCAATCACTTCTTCACTGTGCCGTTCCTGAAAGATGTTGTCAGTGTTTACGAACCTCA
ATTGCAGCACCATGTGGCTCAGAAGAAGATTCCATATGTGGATTCCCAGGGCCACTTAATTAAGCCAGACAAGCCAAATG
GAATAAAGATGGAAAAATTAGTCTTTGACATCTTCCAGTTTGCAAAGAAGTTTGTGGTGTACGAAGTATTACGGGAAGAC
GAATTCTCCCCGCTCAAAAATGCAGACAGTCAGAATGGGAAGGACAACCCGACCACTGCAAGGCATGCCTTGATGTCCCT
TCACCATTGCTGGGTCCTCAATGCTGGGGGACACTTCATAGATGAAAATGGCTCCCGCCTCCCAGCCATCCCCCGCAGTG
CTACAAATGGAAAGTCAGAGACCATCACAGCTGATGTCAATCACAAATTGAAGGATGCCAATGATGTGCCGATCCAGTGT
GAGATCTCTCCCCTCATCTCTTACGCTGGAGAAGGGCTTGAAGGCTATGTGGCAGATAAAGACTTCCATGCACCCTTAAT
CATCGATGAGAACGGAGTTCATGAGCTGGTGAAAAATGGCATA

Alignment

ORF - retro_rnor_2277 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.31 %
• Parental protein coverage: 99.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVNDLRQRLSAAGQQHLLQFWSELSEAQQGELYMELQAMNFEELNSFFQKAVGEFDRSSHQEKVDARMEP
          NVNDLRQRLSAAGQQHLLQFW.ELSEAQQGELYMELQAMNFEE.NSFFQKAVGEFDRSSHQEKVDARMEP
Retrocopy NVNDLRQRLSAAGQQHLLQFWNELSEAQQGELYMELQAMNFEEPNSFFQKAVGEFDRSSHQEKVDARMEP

Parental  VPRQVLGSATRDQDQLQAWESEGLSQISQNKVAVLLLAGGQGTRLGVTYPKGMYDVGLPSHKTLFQIQAE
          VPRQVLGSATRDQDQLQAWES.GLSQISQNKVAVLLLAGGQG..LGVTYPKGMYDVGLPSHKTLFQIQAE
Retrocopy VPRQVLGSATRDQDQLQAWESQGLSQISQNKVAVLLLAGGQGSSLGVTYPKGMYDVGLPSHKTLFQIQAE

Parental  RILKLQQLAEKQYGNKCTIPWYIMTSGRTMESTKEFFTKHKFFGLKKENVVFFQQGMLPAMSFDGKVILE
          RILKLQQLAEKQYGNKC.IPWYIM.SGRTMES.KEFFTKHKFFGLKKENVVFFQQGMLPAMSFDGKVILE
Retrocopy RILKLQQLAEKQYGNKCIIPWYIMASGRTMESMKEFFTKHKFFGLKKENVVFFQQGMLPAMSFDGKVILE

Parental  EKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVE
          EKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVE
Retrocopy EKNKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKVADPRFIGFCIQKGADCGAKVVE

Parental  KTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGRLLFNAGNIANHFFTVPFLKDVVNVYEPQLQH
          KTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDG.L.FNAGNIANHFFTVPFLKDVV.VYEPQLQH
Retrocopy KTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKRSSDGGLQFNAGNIANHFFTVPFLKDVVSVYEPQLQH

Parental  HVAQKKIPYVDSQGHLIKPDKPNGIKMEKFVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTA
          HVAQKKIPYVDSQGHLIKPDKPNGIKMEK.VFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTA
Retrocopy HVAQKKIPYVDSQGHLIKPDKPNGIKMEKLVFDIFQFAKKFVVYEVLREDEFSPLKNADSQNGKDNPTTA

Parental  RHALMSLHHCWVLNAGGHFIDENGSRLPAIPR-ATNGKSETITADVNHNLKDANDVPIQCEISPLISYAG
          RHALMSLHHCWVLNAGGHFIDENGSRLPAIPR.ATNGKSETITADVNH.LKDANDVPIQCEISPLISYAG
Retrocopy RHALMSLHHCWVLNAGGHFIDENGSRLPAIPRSATNGKSETITADVNHKLKDANDVPIQCEISPLISYAG

Parental  EGLEGYVADKDFHAPLIIDENGVHELVKNGI
          EGLEGYVADKDFHAPLIIDENGVHELVKNGI
Retrocopy EGLEGYVADKDFHAPLIIDENGVHELVKNGI

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	0.29 RPM	16.03 RPM
SRP017611_kidney	0.49 RPM	13.75 RPM
SRP017611_liver	0.20 RPM	9.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2277 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2277 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189, retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035,
Rattus norvegicus	ENSRNOG00000002926	1 retrocopy	retro_rnor_2277 ,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582,