RetrogeneDB ID: retro_ocun_1153

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:4046465..4047165(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSPO2
• Ensembl ID: ENSOCUG00000000779
• Aliases: None
• Description: R-spondin 2 [Source:HGNC Symbol;Acc:28583]

Sequence

>retro_ocun_1153
AGGTTCTGCTCGCGCTGAACTGACGCATTCGGCCCCCGGGGTTGCGTTGACTCACCCTCGGAGTCCTCCCCAGCAGCGCG
CTGGTGCCAGCCTCTTGGATGAGCCCTCCAGGTCCCCGACTTTGAGAGGCGCCTCTCCCCAGCCAACCGTCCAGATGCAG
TTTCACCTCTTCTCCTTTGTGCTCATCATTCTGAACTGTATGGATTACAGCCACTGTCAAGGCAACCGATGGAGACACAA
TAAGCGAGCTAGTTATGTATCAAACCCTATTTGCAAAGGTTGCTTGTCTTTTTCAAAGGACAATGGGTGCAGCTGATGTC
AACAGAAACTGTTCTTCCTTCGAAGAGAAGGGATGCGCCAATATGGAGAGTGCCTGCATTCCTGCCCGTCAGGGTACTAT
GGACACCGAGCCCCAGATATGAACAGAAGTGCAAGATGCAGAATAGAAAACTGTGATTCTTGCTTTAGCAAAGACCTTTG
TACCAAGTGCAAAGTAGGCTTCTACCTGCATAGAGGCCTCTGCTTTGATGAACGTCCAGATGGTTTTGCACCATTAGATG
AAACCATGGAGTGCGTGCAAGGATGTGAAGTTGGTCATTGGAGTGAATGGGGAACTTGTAGCAGAAATAATTGCACATGT
GGATTTAAATGGGGCCTGGAAACCAGAATACGGCAAATTGTTAAAAAGCCTGCAAAAGAA

Alignment

ORF - retro_ocun_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.94 %
• Parental protein coverage: 50.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RCCSRRTDACGP-GLAATRPPSPPQQRAGAGFLDEPSSSPTLRGASPQSTVQMQFRLFSFALIILNCMDY
          R.CSR.TDA.GP.G.A.T.P.SPPQQRAGA..LDEPS.SPTLRGASPQ.TVQMQF.LFSF.LIILNCMDY
Retrocopy RFCSR*TDAFGP>GVALTHPRSPPQQRAGASLLDEPSRSPTLRGASPQPTVQMQFHLFSFVLIILNCMDY

Parental  SHCQGNRWRRNKRASYVSNPICKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAP
          SHCQGNRWR.NKRASYVSNPICKGCLS.SKDNGCS.CQQKL.FFLRREGMRQYGECLHSCPSGYYGHRAP
Retrocopy SHCQGNRWRHNKRASYVSNPICKGCLSFSKDNGCS*CQQKL-FFLRREGMRQYGECLHSCPSGYYGHRAP

Parental  DMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMECVEGCEVGHWSEWGTCSR
          DMNR.ARCRIENCDSCFSKD.CTKCKVGFYLHRG.CFDE.PDGFAPLDETMECV.GCEVGHWSEWGTCSR
Retrocopy DMNRSARCRIENCDSCFSKDLCTKCKVGFYLHRGLCFDERPDGFAPLDETMECVQGCEVGHWSEWGTCSR

Parental  NNRTCGFKWGLETRTRQIVKKPAKD
          NN.TCGFKWGLETR.RQIVKKPAK.
Retrocopy NNCTCGFKWGLETRIRQIVKKPAKE

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	11.81 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1153 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1153 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1153 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000779	1 retrocopy	retro_ocun_1153 ,