RetrogeneDB ID: retro_ocun_181

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:51118530..51119238(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000011845
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005694
• Aliases: None
• Description: None

Sequence

>retro_ocun_181
ATGCGCCGAGGGGCGCCCCAGGACCAGGAGCTGATGGGTCCGGGGGCCCCTGGGCGGGGGTCCCGGAGCGCCCCTCCTCC
CTCGGGACCGGTTGTCCCGGTCCTCGTCTTACCCCTGGATCTAGTATTCAGAGCGGACCAGCGGAGCGGCCTCCGACAGC
TGCTGACCCTCTACAACCCCACAGGAACTGCGCTTTGCTTCCGAGTCCTGTGTACAGCACCTGCGAAATACACGGTGTTT
GAGGCCGAGGGCTATGTGAAGGCGCAGTCCTGCATTGACATAGTGATTCGCCATGTGGCCCCCATCCCCAGCCACTACGA
CGTCCGGGACCGATTCCGCATTGAACTGTCGGAGGAGGGAGCCAATGGCCGAGTGGTGGGCCGCAAGGACATCACCTCGG
TTCTCAGAGCCCCAGCACACCCCCTTGAGCTGCAGGGACAGCCCAACCCGCTGCCCACCCTGGGGCCCCCTGCCGGGACA
GCAGCCCCCACGGCCAGACCCTTCCAAGAGACCCCCCGCCAGCAGCTGGCCACCAGCTCCTTCCTGCTCTTCCTGCTGAC
CGGCATGGTGTCTGTGGCCTTCTTGCTGCTCCCGCTCCAGGACGAAGTGGGCAGCCAGCTGCCCCAGGTCCTGCACGTGT
CCCTGGGACAGAAGCTGGTGGCAGCCTACGTCCTGGGCCTCCTCACCGTGGTGTTTCTCTGGACCTGA

Alignment

ORF - retro_ocun_181 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRGAPQDQELVGPGTPGRGSRSAPPPSGPVVPVLVLPLDLVFRADQRSGLRQLLTLYNPTGTALCFRVL
          MRRGAPQDQEL.GPG.PGRGSRSAPPPSGPVVPVLVLPLDLVFRADQRSGLRQLLTLYNPTGTALCFRVL
Retrocopy MRRGAPQDQELMGPGAPGRGSRSAPPPSGPVVPVLVLPLDLVFRADQRSGLRQLLTLYNPTGTALCFRVL

Parental  CTAPAKYTVFEAEGYVKAQSCIDIVIRHVAPIPSHYDVRDRFRIELSEEGANGRVVGRKDITSVLRAPAH
          CTAPAKYTVFEAEGYVKAQSCIDIVIRHVAPIPSHYDVRDRFRIELSEEGANGRVVGRKDITSVLRAPAH
Retrocopy CTAPAKYTVFEAEGYVKAQSCIDIVIRHVAPIPSHYDVRDRFRIELSEEGANGRVVGRKDITSVLRAPAH

Parental  PLELQGQPNPVPPLGPPAGTAAPMARPFQETPRQQLATSSFLLFLLTGMVSVAFLLLPLQDEVGSQLPQV
          PLELQGQPNP.P.LGPPAGTAAP.ARPFQETPRQQLATSSFLLFLLTGMVSVAFLLLPLQDEVGSQLPQV
Retrocopy PLELQGQPNPLPTLGPPAGTAAPTARPFQETPRQQLATSSFLLFLLTGMVSVAFLLLPLQDEVGSQLPQV

Parental  LHVSLGQKLVAAYVLGLLTVVFLRT
          LHVSLGQKLVAAYVLGLLTVVFL.T
Retrocopy LHVSLGQKLVAAYVLGLLTVVFLWT

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	1.43 RPM	19.59 RPM
SRP017611_kidney	1.22 RPM	15.51 RPM
SRP017611_liver	0.77 RPM	10.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_181 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026246	1 retrocopy	retro_btau_1854,
Myotis lucifugus	ENSMLUG00000010017	1 retrocopy	retro_mluc_1956,
Oryctolagus cuniculus	ENSOCUG00000005694	1 retrocopy	retro_ocun_181 ,
Rattus norvegicus	ENSRNOG00000001396	1 retrocopy	retro_rnor_524,