RetrogeneDB ID: retro_ocun_107

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:143550568..143551213(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000011302
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPL10
• Ensembl ID: ENSOCUG00000015919
• Aliases: None
• Description: ribosomal protein L10 (RPL10), mRNA [Source:RefSeq mRNA;Acc:NM_001171374]

Sequence

>retro_ocun_107
ATGGGCCGCCGCCCCGCCCGGTGTTACCGGTATTGTAAGAACAAGCCGTACCCTAAGTCTCGTTTCTGCCGAGGTGTCCC
TGATGCCAAGATCCATATCTTTGATCTGGGCCGGAAGAAGGCAAAAGTGGATGAGTTTCCACTGTGTGGCCACATGGTGT
CGGATGAATATGAGCAGCTCTCTTCTGAAGCCCTGGAGGCTGCCCGTATTTGTGCCAAAAAATACATGGTAAAAAGCTGT
GGCAAAGATGGCTTTCATATCCGAGTGCGGCTCCACCCCTTCCATGTCATCCGAATCAACAAGATGTTGTCCTGTGCTGG
TGCTGACAGGCTGCAGACAGGTATGTGGGGTGCTTTTGGAAAGCCCCAAGGCACAGTAGCCAGAGTTCACATTGGCCAAG
TCATCATGTCCATCCGCACCAAGCTGCAGAACAAGGAACATGTGGTTGAGGCCCTACGCAGGGCCAAGTTCAAGTTCCCT
GGCCGCCAGAAGATCCACATCTCAAAGAAGTGGGGCTTTACCAAGTTTAACGCGGATGAATTTGAAGACATGGTGGCGGA
GAAGCGGCTCATCCCGGACGGCTGCGGGGTCAAGTACATCCCCAATCGTGGCCCCCTGGACAAGTGGCGGGCCCTCCACT
CATGA

Alignment

ORF - retro_ocun_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
          MGRRPARCYRYCKNKPYPKSRFCRGVPDAKI.IFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI
Retrocopy MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIHIFDLGRKKAKVDEFPLCGHMVSDEYEQLSSEALEAARI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRT
          CA.KYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGM.GAFGKPQGTVARVHIGQVIMSIRT
Retrocopy CAKKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMWGAFGKPQGTVARVHIGQVIMSIRT

Parental  KLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
          KLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR
Retrocopy KLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAEKRLIPDGCGVKYIPNRGPLDKWR

Parental  ALHS
          ALHS
Retrocopy ALHS

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	0.17 RPM	151.44 RPM
SRP017611_kidney	0.10 RPM	394.58 RPM
SRP017611_liver	0.46 RPM	229.99 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_107 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_107 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_107 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011822	5 retrocopies	retro_cjac_156, retro_cjac_174, retro_cjac_260, retro_cjac_277, retro_cjac_61,
Felis catus	ENSFCAG00000011395	1 retrocopy	retro_fcat_81,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,
Oryctolagus cuniculus	ENSOCUG00000015919	2 retrocopies	retro_ocun_107 , retro_ocun_147,
Rattus norvegicus	ENSRNOG00000027149	5 retrocopies	retro_rnor_1007, retro_rnor_1090, retro_rnor_270, retro_rnor_2998, retro_rnor_482,