RetrogeneDB ID: retro_ocun_671

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:124168125..124168652(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT10B
• Ensembl ID: ENSOCUG00000010994
• Aliases: None
• Description: tRNA methyltransferase 10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:26454]

Sequence

>retro_ocun_671
TGTATTGATTTGAGTATGACCCACCATATGTCAAAGAAGCAACTGAGTAGACTGGCTGGACAGATCTGAAGGTTGTATGG
TTCAAACGAGAAGGCTGACAGGCCATTTTGGGTCTACCTCACTGAGTTTACAACAGACAGCCCCTCTATAAAGAGTGTTT
GCGGATGAATGATGGATTTGCTGGTTACCTGCTAGACATAACAGAAGAAAACTACTTTAACTTATTTCCTTTGGAAACCC
TAGTTTACCTGACTCCTGACTCAGAACATGCTTTTGAAGATGTTACTCTAAACAAAGTTTACATCCTTAATGGACTTGTG
GATGAAAGTATTCAGAAGAAAGTAATATTTCAAAAGGCTTGGGAACACTCTGTCAAGACAGCCTGCTTGAAAATACAGGA
ATTCATGGTCAGATGCAAGAATCGGAAAAACTATCATTCAGAGATACTGGCCATCAACCAAGTATTTGATGTCCTGGCCA
CTTACTCTGAGACTCACAATTGGCCTGAAGCCTTGAAGAAAGGAGTC

Alignment

ORF - retro_ocun_671 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.57 %
• Parental protein coverage: 55.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CIDLSMTHHMSKKELSRLAGQIRRLYGSNKKADRPFWIYLTGFTTDSP-LYEECLRMNDGFSSYLLDITE
          CIDLSMTHHMSKK.LSRLAGQI.RLYGSN.KADRPFW.YLT.FTTDSP.LY.ECLRMNDGF..YLLDITE
Retrocopy CIDLSMTHHMSKKQLSRLAGQI*RLYGSNEKADRPFWVYLTEFTTDSP<LYKECLRMNDGFAGYLLDITE

Parental  EDCFNLFPLETLVYLTPDSEHALEDVALNKVYILGGLVDESIQKKVTFQKAWEHSVKTARLPIQEYMVRC
          E..FNLFPLETLVYLTPDSEHA.EDV.LNKVYIL.GLVDESIQKKV.FQKAWEHSVKTA.L.IQE.MVRC
Retrocopy ENYFNLFPLETLVYLTPDSEHAFEDVTLNKVYILNGLVDESIQKKVIFQKAWEHSVKTACLKIQEFMVRC

Parental  QNGKNYHSEILAINQVFDVLATYFETHSWPEALKKGV
          .N.KNYHSEILAINQVFDVLATY.ETH.WPEALKKGV
Retrocopy KNRKNYHSEILAINQVFDVLATYSETHNWPEALKKGV

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	9.33 RPM
SRP017611_kidney	0.00 RPM	6.39 RPM
SRP017611_liver	0.00 RPM	2.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_671 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_671 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
Oryctolagus cuniculus	ENSOCUG00000010994	1 retrocopy	retro_ocun_671 ,
Oryctolagus cuniculus	ENSOCUG00000015213	1 retrocopy	retro_ocun_1482,
Pongo abelii	ENSPPYG00000019056	1 retrocopy	retro_pabe_3287,