RetrogeneDB ID: retro_rnor_85

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:60898257..60900042(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Esco2
• Ensembl ID: ENSRNOG00000015921
• Aliases: None
• Description: Protein Esco2 [Source:UniProtKB/TrEMBL;Acc:D4ABF1]

Sequence

>retro_rnor_85
ATGATGGCAACTTTTACTCCAAGGAAGAGGAAGCGACATACACTGAAGGCTGATAATGATGATAGCCTATTAACAGATAT
TTCATCAAGCAAACTAAGATTTGCTGAAAATCTATATTCATCACCTAATAAGAAACATAATTGTCAAAGCAGTGTTCAAA
AGGAAGAAAAGCCATGCTCCCACCAACGACATTTCTCTTCAAGTCCACTCAAAACAACTGAAAATAATATGTTGTCATTT
GCAAACCACAGCTCGTTATTTAAACCAGTTGTGTCTACTGTATCTTTCTACAATAAAAATAAGCACTACCTCAATCCACT
GGAGAGGAAGTTGATAAGAGAGTGTAAATCTATTTGTCTAGCAACTAAAAATGAAGATAGACCTTTTCCCAGTGTGACAG
AAAAAATTCAGAGAAAACCAGTCTGTACCAAGAATAAAAAAAGGCAGAAGAGTTTAACTGCTAATCATCAACCAAATTAC
AAGCACGTCAAGTCTATATCAAGAAACCTGAAAAATTCCAAGCCAAGTCAAGTGACCTATAAGCCAGTTGTGGACAAAGA
GAACAGTTGTTTTCCCACAGAAAATCCTCCAAATTCTCCTCCTCGGGTTCTAAGCCAGAAAATAAGACCACGAGTTACAC
TCCAAGGTGGAGCAGCATTTTTTGTTAGAAAAAGAAACTTTCTTAAAAAGTCACCTCTAGAAGATAAGCCATTACCAATA
CTTTTGCAGAAAAATGAACCAGAGGTCACTGAAGATGCCCTTGAGGCAAAGCAAGTCCCAAAGTCCTTGTTAGTGGGAGA
GAAATCAAATGTTGAGCTACTAGACGCAAGAAGTGAAAGTGAAGAGAAACTGGGAAAGAATTCCTCAGGTGCAGTAGTTT
CTTCAAAGGAGTGTAAACTTGATAAACATAATTTTCCTTCAGAGAAGTCACTTGAGAACAAGACAATTTCTTCGGAGTCT
GTCTATTCTATCTTCAGTGTTTCTTCAACGAACACAAAAAGGTCTCCATCTGAAGAACAGTCTTCTGTGGGATCCCCTGC
ATGTACTAACTTCTTGAAACAGACAAATGTACAGAAAAATATTAATTTCAGAGATACAAATAAAGGAGGAAAAGACCAGC
TTGTTATTGACGCGAGTCAGAAACATTTTGGGACGACTATGTGTAAGTCTTGTGGCATGATCTATACTGCTTCCAACCCT
GAAGATGAAATACAACATCTCCAACATCACCACCGATTTCTGGAGGGAATTAAATATGTGGGATGGAAAAGAGAACGGAT
AGTAGCAGAGTTTTGGGATGGGAAGATTGTGTTGGTCCTGCCACGTGATCCAAGTTATGCCATCAAAAAGGTAGAGGATG
TCCAAGAACTTGTGGATCTGGAATTGGGTTTCCAGCAAGTTGTTCCCATGTGTCCAAACAAAACCAAAACCTTCCTCTTT
ATTGATGAAAAGAGAGTAGTTGGATGTTTAATTGCGGAACCCATCAAACAGGCCTTTCGTGTCCTGTCAGAACCAAGTAC
CACTAAAGAATGTTCTAGAGCTTGGCGGTGTTCAGATGTACCAGAACCTGCAATTTGTGGAATAAGTAGAATCTGGGTCT
TCAAACTAAAAAGAAGAAAACGCATTGCAAGACGACTGGTTGACACTGTCAGGAATTGCTTCATGTTTGGCTGTTTCCTC
AGCATTAATGAAATTGCATTTTCTGACCCAACACCAGATGGCAAATTATTTGCAACCAAGTATTGCAACACCCCTAATTT
CCTTGTATATAATTTTCATAGCTAA

Alignment

ORF - retro_rnor_85 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.16 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMATFTPRKRKRHTLKADNDDSLLTDISSSKLRFAENLYSSPNKKHNCQSSVQKEEKPCSHQRHFSSSPL
          MMATFTPRKRKRHTLKADNDDSLLTDISSSKLRFAENLYSSPNKKHNCQSSVQKEEKPCSHQRHFSSSPL
Retrocopy MMATFTPRKRKRHTLKADNDDSLLTDISSSKLRFAENLYSSPNKKHNCQSSVQKEEKPCSHQRHFSSSPL

Parental  KTTENNMLSFANHSSLFKPVVSTVSFYNKNKHYLNPLERKLIRECKSICLATKNEDKPFPSVTEKIQRKP
          KTTENNMLSFANHSSLFKPVVSTVSFYNKNKHYLNPLERKLIRECKSICLATKNED.PFPSVTEKIQRKP
Retrocopy KTTENNMLSFANHSSLFKPVVSTVSFYNKNKHYLNPLERKLIRECKSICLATKNEDRPFPSVTEKIQRKP

Parental  VCTKNKKRQKSLTANHQPNYKHVKSISRNLKNSKPSQVTYKPVVDKENSCFPPENPPNSPPRVLSQKIRP
          VCTKNKKRQKSLTANHQPNYKHVKSISRNLKNSKPSQVTYKPVVDKENSCFP.ENPPNSPPRVLSQKIRP
Retrocopy VCTKNKKRQKSLTANHQPNYKHVKSISRNLKNSKPSQVTYKPVVDKENSCFPTENPPNSPPRVLSQKIRP

Parental  RVTLQGGAAFFVRKRNFLKKSPLEDKPLPILLQKNEPEVTEDALEAKQVPKSLLVGEKSNVELLDARSES
          RVTLQGGAAFFVRKRNFLKKSPLEDKPLPILLQKNEPEVTEDALEAKQVPKSLLVGEKSNVELLDARSES
Retrocopy RVTLQGGAAFFVRKRNFLKKSPLEDKPLPILLQKNEPEVTEDALEAKQVPKSLLVGEKSNVELLDARSES

Parental  EEKLGKNSSGAVVSSKECKLGKHNFPSEKSLENKTISSESVYSIFSVSSTNTKRSPSEEQSSVGSTACTN
          EEKLGKNSSGAVVSSKECKL.KHNFPSEKSLENKTISSESVYSIFSVSSTNTKRSPSEEQSSVGS.ACTN
Retrocopy EEKLGKNSSGAVVSSKECKLDKHNFPSEKSLENKTISSESVYSIFSVSSTNTKRSPSEEQSSVGSPACTN

Parental  FLKQTNVQKNINFRDTNKGGKDQLVIDAGQKHFGTTMCKSCGMIYTASNPEDEIQHLQHHHRFLEGIKYV
          FLKQTNVQKNINFRDTNKGGKDQLVIDA.QKHFGTTMCKSCGMIYTASNPEDEIQHLQHHHRFLEGIKYV
Retrocopy FLKQTNVQKNINFRDTNKGGKDQLVIDASQKHFGTTMCKSCGMIYTASNPEDEIQHLQHHHRFLEGIKYV

Parental  GWKRERIVAEFWDGKIVLVLPRDPSYAIKKVEDVQELVDLELGFQQVVPMCPNKTKTFLFIDEKRVVGCL
          GWKRERIVAEFWDGKIVLVLPRDPSYAIKKVEDVQELVDLELGFQQVVPMCPNKTKTFLFIDEKRVVGCL
Retrocopy GWKRERIVAEFWDGKIVLVLPRDPSYAIKKVEDVQELVDLELGFQQVVPMCPNKTKTFLFIDEKRVVGCL

Parental  IAEPIKQAFRVLSEPSTTKECSRAWRCSDVPEPAICGISRIWVFKLKRRKRIARRLVDTVRNCFMFGCFL
          IAEPIKQAFRVLSEPSTTKECSRAWRCSDVPEPAICGISRIWVFKLKRRKRIARRLVDTVRNCFMFGCFL
Retrocopy IAEPIKQAFRVLSEPSTTKECSRAWRCSDVPEPAICGISRIWVFKLKRRKRIARRLVDTVRNCFMFGCFL

Parental  SINEIAFSDPTPDGKLFATKYCNTPNFLVYNFHS
          SINEIAFSDPTPDGKLFATKYCNTPNFLVYNFHS
Retrocopy SINEIAFSDPTPDGKLFATKYCNTPNFLVYNFHS

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	0.00 RPM	0.14 RPM
SRP017611_kidney	0.00 RPM	0.14 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_85 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_85 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_85 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000001229	1 retrocopy	retro_lafr_978,
Rattus norvegicus	ENSRNOG00000014031	1 retrocopy	retro_rnor_956,
Rattus norvegicus	ENSRNOG00000015921	1 retrocopy	retro_rnor_85 ,