RetrogeneDB ID: retro_rnor_2129

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:19870105..19871674(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000008861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cyld
• Ensembl ID: ENSRNOG00000014048
• Aliases: Cyld, LRRGT00003, Rp1, Rp1h
• Description: ubiquitin carboxyl-terminal hydrolase CYLD [Source:RefSeq peptide;Acc:NP_001017380]

Sequence

>retro_rnor_2129
TCACAGTCCACTCTCTCTCTGTCAGTGCAGTCTGTGATGGGGGAGCTGAACAGCACGCCTGTCCAGGAGAGTCCACCCTT
GCCCAGCTCTTCTGGGAATGGACACGGGCTAGAGGTGGGCTCACTGGCTGAAGTAAAAGAGAACCCCCCGTTCTATGGGG
TTATCCGTTGGATTGGCCAGCCACCAGGGCTCAGTGACGTGCTCGCTGGATTGGAACCGGAAGATGAATGCGCAGGTTGC
ACGGATGGAACTTTCAGGGGCACGCGCTATTTCACCTGTGCCCTGAAGAAAGCACTGTTCGTGAAACTGAAGAGCTGCAG
ACCAGACTCTAGGTTTGCATCCTTGCAGCCTGTTTCCAATCAGATCGAAAGGTGTAACTCTTTAGCATTTGGGGGCTACT
TAAGTGAAGTAGTAGAAGAAAATACGCCACCTAAAATGGAAAAGGAAGGTTTAGAGATAATGATTGGAAAGAAGAAAGGC
ATCCAGGGCCATTACAATTCTTGTTACTTAGACTCAACTTTATTCTGCTTATTTGCTTTTAGTTCTGCCCTGGACACTGT
ATTACTTAGACCCAAAGAGAAGAATGACGTAGAGTATTACAGTGAGACTCAAGAGCTACTGAGGACAGAGATAGTCAATC
CTCTGAGAATATATGGATATGTGTGTGCCACAAAGATTATGAAGCTGAGGAAAATACTTGAAAAAGTTGAGGCTGCATCA
GGATTTACCTCTGAGGAAAAAGATCCTGAAGAATTTCTAAACATCCTGTTTCATGATATTTTAAGGATTGAACCATTGTT
AAAAATATGGTCAGCAGGTCAAAAAGTTCAAGACTGTAACTTCTATCAAATTTTTATGGAAAAAAATGAGAAAGTCGGAG
TACCCACAATCCAGCAGTTATTAGAATGTTCTTTTATCAACAGCAACCTGAAATTTGCGGAGGCACCATCATGCTTGATT
ATCCAGATGCCTTGGTTTGGGAAAGACTTTAAACTATTTAAAAAATTTTTTCCTTCCCTGGAATTAAATATGACAGATTT
ACTTGAAGACACTCCCAGGCAGTGCCGCATCTGTGGAGGACTCGCCATGTATGAGTGTAGAGAGTGCTATGATGACCCGG
ACATCTCGGCAGGGAAGATCAAGCAGTTCTGTAAGACCTGCAGCACTCAGGTTCACCTTCATCCCAGAAGACTGAATCAC
ACTTACCATCCAGTATCACTTCCCAAAGACTTGCCCGACTGGGACTGGAGACATGGCTGCATCCCATGTCAGAAGATGGA
GTTATTTGCTGTGCTCTGCATAGAAACCAGCCACTATGTTGCTTTTGTGAAGTACGGGAAGGATGACTCTGCCTGGCTCT
TCTTTGACAGCATGGCTGATCGAGATGGTGGTCAGAATGGCTTCAACATTCCACAAGTGACACCCTGCCCAGAAGTAGGA
GAGTACTTGAAGATGTCTCTGGAGGACCTGCACTCTTTGGACTCCAGAAGGATTCAAGGCTGTGCGCGCAGACTTCTTTG
CGATGCATACATGTGCATGTACCAGAGTCCAACCATGAGCTTGTACAAA

Alignment

ORF - retro_rnor_2129 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.71 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHSPLSLSVQSVMGELNSTPVQESPPMPSSSGNAHGLEVGSLAEVKENPPFYGVIRWIGQPPGLSDVLAG
          ..S.LSLSVQSVMGELNSTPVQESPP.PSSSGN.HGLEVGSLAEVKENPPFYGVIRWIGQPPGLSDVLAG
Retrocopy SQSTLSLSVQSVMGELNSTPVQESPPLPSSSGNGHGLEVGSLAEVKENPPFYGVIRWIGQPPGLSDVLAG

Parental  LELEDECAGCTDGTFRGTRYFTCALKKALFVKLKSCRPDSRFASLQPVSNQIERCNSLAFGGYLSEVVEE
          LE.EDECAGCTDGTFRGTRYFTCALKKALFVKLKSCRPDSRFASLQPVSNQIERCNSLAFGGYLSEVVEE
Retrocopy LEPEDECAGCTDGTFRGTRYFTCALKKALFVKLKSCRPDSRFASLQPVSNQIERCNSLAFGGYLSEVVEE

Parental  NTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDVEYYSETQELLRTE
          NTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDVEYYSETQELLRTE
Retrocopy NTPPKMEKEGLEIMIGKKKGIQGHYNSCYLDSTLFCLFAFSSALDTVLLRPKEKNDVEYYSETQELLRTE

Parental  IVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRVEPLLKIRSAGQKVQDCN
          IVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILR.EPLLKI.SAGQKVQDCN
Retrocopy IVNPLRIYGYVCATKIMKLRKILEKVEAASGFTSEEKDPEEFLNILFHDILRIEPLLKIWSAGQKVQDCN

Parental  FYQIFMEKNEKVGVPTIQQLLEWSFINSNLKFAEAPSCLIIQMPRFGKDFKLFKKIFPSLELNITDLLED
          FYQIFMEKNEKVGVPTIQQLLE.SFINSNLKFAEAPSCLIIQMP.FGKDFKLFKK.FPSLELN.TDLLED
Retrocopy FYQIFMEKNEKVGVPTIQQLLECSFINSNLKFAEAPSCLIIQMPWFGKDFKLFKKFFPSLELNMTDLLED

Parental  TPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHTYHPVSLPKDLPDWDWRHGC
          TPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHTYHPVSLPKDLPDWDWRHGC
Retrocopy TPRQCRICGGLAMYECRECYDDPDISAGKIKQFCKTCSTQVHLHPRRLNHTYHPVSLPKDLPDWDWRHGC

Parental  IPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDL
          IPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDL
Retrocopy IPCQKMELFAVLCIETSHYVAFVKYGKDDSAWLFFDSMADRDGGQNGFNIPQVTPCPEVGEYLKMSLEDL

Parental  HSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK
          HSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK
Retrocopy HSLDSRRIQGCARRLLCDAYMCMYQSPTMSLYK

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	0.22 RPM	44.86 RPM
SRP017611_kidney	0.00 RPM	11.37 RPM
SRP017611_liver	0.00 RPM	4.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2129 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2129 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000014048	1 retrocopy	retro_rnor_2129 ,