RetrogeneDB ID: retro_ocun_866

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:36406315..36407068(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023474
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MRPS35
• Ensembl ID: ENSOCUG00000016214
• Aliases: None
• Description: mitochondrial ribosomal protein S35 [Source:HGNC Symbol;Acc:16635]

Sequence

>retro_ocun_866
AGCGTTTACCCTGTGGCAGCGCCATTTAAACCCTCTATAGTCCCTCTTCCTTTCGAATGGGTTATCCTGTGAAAAAGGGT
GTGCCCATGGCAAAAGAGAGCAATCTAGAACCCCTGAAGATCCCCAGTTTTCTGCATTTGACTCCTGTAGCGATTAAAAA
GCGCTGTGAAGTTCTTAAAGATTTCTGACCGAGTGGCCAGCCGCACTTGACACTGATGAGAAATGTGAGAAGCAGTTTCC
AATTGAAATTGACACAGCTGCCTACGTTTCACCAGGACCCTCCGTTCCCAACCCTAAGGCACGAACCTTAAGGGTTAAAC
TTTCCAGTTTGAATTTAGATGACCATGCAAAGAAGAAGTTGATTAAACTTGTAGGAGAACGATCCCGCAAGACCAGTGAT
TTGCTCACCCTCAGAACAGACAGCTGTCCTTTAAAGAGACAGAATTACGACTACGCAATATATCTACTAACAGTTTTATA
CCTTGAGTCTTGGGAAACTGAATGGGAAAAATATAAAAGTGAGGCAGACATGGAGAAGTATGAATGGAAAAATAGCTCCT
GAGAAAAAATATCCTGGAAACGCTTCTGCAAATGAGAGCTGCTGAGAAGACAGGCGCCAGAGGAGAGGAGCTCCCGGCTA
CCAAGGAAGTGGGCGATGACGGGCGATCTGTTCTCCGTCTGAAGAATGAGGGCGACAGCGAAAAGACCCTTTCACAGTAC
AAAGAATCCGTGAAGAGACTGTTAAACTTGACA

Alignment

ORF - retro_ocun_866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.05 %
• Parental protein coverage: 78.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVYPVAAPFKPSVVPLPV-RMGYPVKKGVPMAKEGNLELLKIPNFLHLTPVAIKKHCEVLKDF-CTEWPA
          SVYPVAAPFKPS.VPLP..RMGYPVKKGVPMAKE.NLE.LKIP.FLHLTPVAIKK.CEVLKDF..TEWPA
Retrocopy SVYPVAAPFKPSIVPLPF<RMGYPVKKGVPMAKESNLEPLKIPSFLHLTPVAIKKRCEVLKDF<LTEWPA

Parental  ALDTDEKCEKHFPIEIDTAAYVSSGPSIRNPKARTVTLRVKLSSLNLDDHAKKKLIKLAGERYCKTSDVL
          ALDTDEKCEK.FPIEIDTAAYVS.GPS..NPKAR..TLRVKLSSLNLDDHAKKKLIKL.GER..KTSD.L
Retrocopy ALDTDEKCEKQFPIEIDTAAYVSPGPSVPNPKAR--TLRVKLSSLNLDDHAKKKLIKLVGERSRKTSDLL

Parental  TIRTDRCPLKRQNYDYAIYLLTVLYHESWKTEEWEKYKSEADMEEYEWKNSSSE-KNILDTLLQMRAAEK
          T.RTD.CPLKRQNYDYAIYLLTVLY.ESW.T.EWEKYKSEADME.YEWKNSS.E.KNIL.TLLQMRAAEK
Retrocopy TLRTDSCPLKRQNYDYAIYLLTVLYLESWET-EWEKYKSEADMEKYEWKNSS*E<KNILETLLQMRAAEK

Parental  TSASGEELLATKEVDDYRRSVVSLKNEGDSEKTLSQYKESVKRLLNLT
          T.A.GEEL.ATKEV.D..RSV..LKNEGDSEKTLSQYKESVKRLLNLT
Retrocopy TGARGEELPATKEVGDDGRSVLRLKNEGDSEKTLSQYKESVKRLLNLT

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	15.56 RPM
SRP017611_kidney	0.00 RPM	29.29 RPM
SRP017611_liver	0.00 RPM	6.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_866 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_866 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_866 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005034	1 retrocopy	retro_etel_2145,
Loxodonta africana	ENSLAFG00000010490	1 retrocopy	retro_lafr_449,
Oryctolagus cuniculus	ENSOCUG00000016214	1 retrocopy	retro_ocun_866 ,
Otolemur garnettii	ENSOGAG00000010630	2 retrocopies	retro_ogar_1121, retro_ogar_2807,