RetrogeneDB ID: retro_rnor_852

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:6242420..6243802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uba3
• Ensembl ID: ENSRNOG00000006221
• Aliases: Uba3, Ube1c
• Description: NEDD8-activating enzyme E1 catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:Q99MI7]

Sequence

>retro_rnor_852
ATGGCGGATGGCGAGGAGCTGGAGAAGAAAAGTAGGAGAATAGAGGAGCTGCTGGCTGAGAAAATGGCTGTTGATGGTGG
GTGTGGGGACACTGGAGACTGGGAAGGTCGCTGGAACCATGTAAAGAAGTTCCTTGAGTGGCCTGGACCCTTCATACACC
CTGATTTCGAACCGAGCACTGAATCACTCCAGTTCTTGTTAGATACATGTAAAGTTCTAGTCATTGGAGCTGGTGGCTTA
GGATGTGAGCTTCTGAAAAATCTGGCATTGTCTGGTTTTAGACAGATTCATGTTATAGACATGGACACTATAGATGTTTC
CAATTTAAATAGTCAGTTTTTATTTAGGCCTAAAGATGTTGGAAGACCCAAGGCTGAAGTTGCTGCAGAATTCCTGAATG
ACAGAGTTCCTAACTGCAACGTGGTCCCACATTTCAACAAGATTCAAGACTTTAACGACACTTTCTACCTACAATTTCAT
ATTATCGTATGTGGCCTGAACTCTATCATAGCCAGGAGATGGATCAATGGAATGCTGATATCTCTTCTAAATTATGAAGA
TGGTGTGTTGGATCCAAGCTCCATTGTACCTTTGATAGATGGGGGGACAGAAAGCTTTAAAGGGAATGCCCGAATGATTT
TTGCCTGGAATGACCACTTGTATTGAGTGCACTCTGGAACTTTACCCACCACAGGTCAATTTCCCCATGTGTACCACTGC
ATCTATGTCCAGGCTCCCAGAGCACTGTATCGAGTATGTAAGGACGTTGCAATGGCCTAAAGAGCAGCCTTTTGGAGATG
GGGTTTCATTAGATGGAGATGACCCTGAACATAGTCAGTGGATTTTCCAAAAGTCTGTAGAGAGAGCATCACAATATAAT
ATTAGAGGTGTTACCTACAGACTCTCTCAAGGGGTAGTAAAACGAATCATTCCTGCAGTAGCTTCTACAAATGCAGTCAT
TGCAGCTGTGTGTGCCACTGAGGTTTTCAAGATAGCTACAAGTGCGTACATCCCCCTTAATAACTACTTAGTATTCAATG
ATGTAGATGGACTGTACATTTACACATTTGAGCAGAGAGAAAGGAGAACTGTCCTGTGTGTAGCCAGCTTCCTCAAAACA
TCCAGTTCTCCCCAACAGCTAAACTGCAAGAGGTCTTAGACTATCTAACCAACAGTGCTTCTCTGCAAATGAAGTCTCCA
GCTATAACAGCCACATTAGAGGGAGAAAACAGGACACTTTACAGTCAGTAATGTCTATTGAAGAACGAACGAGACCGAAT
CTGTCCAAAACATTAAAAGAGCTGGGACTAGTTGATGGACAAGAACTGGCTGTTGCTGATGTCACCACACCACAAACTGT
ACTATTTAAACTTCATTTTACT

Alignment

ORF - retro_rnor_852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADGEEPEKKRRRIEELLAERMAVDGGCGDTGDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTC
          MADGEE.EKK.RRIEELLAE.MAVDGGCGDTGDWEGRWNHVKKFLE..GPF.HPDFEPSTESLQFLLDTC
Retrocopy MADGEELEKKSRRIEELLAEKMAVDGGCGDTGDWEGRWNHVKKFLEWPGPFIHPDFEPSTESLQFLLDTC

Parental  KVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDVGRPKAEVAAEFLNDRVPNCN
          KVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLN.QFLFRPKDVGRPKAEVAAEFLNDRVPNCN
Retrocopy KVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNSQFLFRPKDVGRPKAEVAAEFLNDRVPNCN

Parental  VVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNA
          VVPHFNKIQDFNDTFY.QFHIIVCGL.SIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTE.FKGNA
Retrocopy VVPHFNKIQDFNDTFYLQFHIIVCGLNSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTESFKGNA

Parental  RVI-LPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGDGVPLDGDDPEHIQ
          R.I.LPGMT.CIECTLELYPPQVNFPMCT.ASM.RLPEHCIEYVR.LQWPKEQPFGDGV.LDGDDPEH.Q
Retrocopy RMI>LPGMTTCIECTLELYPPQVNFPMCTTASMSRLPEHCIEYVRTLQWPKEQPFGDGVSLDGDDPEHSQ

Parental  WIFQKSVERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVD
          WIFQKSVERASQYNIRGVTYRL.QGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVD
Retrocopy WIFQKSVERASQYNIRGVTYRLSQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVD

Parental  GLYTYTFE-AERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITAT-LEGKNRTLYLQS
          GLY.YTFE.AERKENCP.CSQLPQNIQFSP.AKLQEVLDYLTNSASLQMKSPAITAT...G......LQS
Retrocopy GLYIYTFE<AERKENCPVCSQLPQNIQFSPTAKLQEVLDYLTNSASLQMKSPAITAT<IRGRKQDT-LQS

Parental  VTSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFT
          V.SIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFT
Retrocopy VMSIEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFT

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	0.72 RPM	42.78 RPM
SRP017611_kidney	0.49 RPM	37.75 RPM
SRP017611_liver	0.40 RPM	17.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_852 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_852 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852 ,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192,