RetrogeneDB ID: retro_ocun_1587

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018705:3093767..3094785(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000009013
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC40
• Ensembl ID: ENSOCUG00000001223
• Aliases: None
• Description: cell division cycle 40 [Source:HGNC Symbol;Acc:17350]

Sequence

>retro_ocun_1587
ATCTTACATGTTAAAGAAATGTATGACTATCAAGGCAGGTGCTACCTTCACATACCTCAGGATGTTGGTGTAAATCTACG
GTCAAGTGTGCCACCTGAGAAGTGTTATCTTCCCAAAAAACAGATTCACATATGGTCTGGACACACCAAGGGCGTCAGTG
CAGTCAGACTGTTTCCTCTCTCTGGCCATTTGTTGCTGTCTTGCTCCATGGACTGTAAAATTAAGTTGTGGGAGGTTTAT
GGAGACCGCTGCTGTCTGAGAACATTTATTGGTCACAGTAAAGCCGAAGGGACATCTGCTTCAACACCGCAGGAACACAG
TTTCGTAGTGCAGCCTATGACAGACACCTGAAGCTCTGGGACACTGAGACAGGACAGTGTATATCAAGATTTACAAACCG
AAAAGTGCCCTACTGTGTCAAATTCAATCCTGATGAAGACAAGCAAAATCTCTTTGTGCCTGGGATGTCTGATAAAAAGA
TTGTGCAATGGGACATTCGAAGTGGAGAAATTGTGCAGGAATATGATCGGCATTTGGGAGCTGTCAATACCATTGTTTTT
GTTGATGAAAACAGGAGATTTGTTAGTACATCTGATGATAAGAGCCTAAGAGTTTGGGAATGGGACATCCCTGTGGATTT
CAAGTATATAGCAGAACCCAGTATGCACTCAATGCCTGCAGTGACTTTGTCTCCAAATGGGAAATGGCTAGCATGCCAAT
CAATGGACAACCAAATCTTAATTTTTGGAGCCCAGAACAGATTTAGATTAAATAAGAAAAAAATTTTTAAGGGCCACATG
GTAGCAGGTTATGCTTGTCAGGTGGACTTTTCACCAGACATGAGCTATGTGATTTCAGGAGATGGAAATGGAAAATTAAA
CATTTGGGACTGGAAGACCACAAAACTCTATAGTCAGTTTAAAGCTCATGATAAAGTGTGTATAGGCGCAGTGTGGCACC
CTCAAGAAACATCTAAAGTCATAACGTGCAGCTGGGTGGTCTGATTAAACTGTGGGAT

Alignment

ORF - retro_ocun_1587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.49 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILHVKEMYDYQGRSYLHIPQDVGVNLRSSVPPEKCYLPKKQIHIWSGHTKGVSAVRLFPLSGHLLLSCSM
          ILHVKEMYDYQGR.YLHIPQDVGVNLRSSVPPEKCYLPKKQIHIWSGHTKGVSAVRLFPLSGHLLLSCSM
Retrocopy ILHVKEMYDYQGRCYLHIPQDVGVNLRSSVPPEKCYLPKKQIHIWSGHTKGVSAVRLFPLSGHLLLSCSM

Parental  DCKIKLWEVYGDRRCLRTFIGHSKAV-RDICFNTAGTQFLSAAYDRYLKLWDTETGQCISRFTNRKVPYC
          DCKIKLWEVYGDR.CLRTFIGHSKA..RDICFNTAGTQF.SAAYDR.LKLWDTETGQCISRFTNRKVPYC
Retrocopy DCKIKLWEVYGDRCCLRTFIGHSKAE<RDICFNTAGTQFRSAAYDRHLKLWDTETGQCISRFTNRKVPYC

Parental  VKFNPDEDKQNLFVAGMSDKKIVQWDIRSGEIVQEYDRHLGAVNTIVFVDENRRFVSTSDDKSLRVWEWD
          VKFNPDEDKQNLFV.GMSDKKIVQWDIRSGEIVQEYDRHLGAVNTIVFVDENRRFVSTSDDKSLRVWEWD
Retrocopy VKFNPDEDKQNLFVPGMSDKKIVQWDIRSGEIVQEYDRHLGAVNTIVFVDENRRFVSTSDDKSLRVWEWD

Parental  IPVDFKYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKIFKGHMVAGYACQVDFSP
          IPVDFKYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKIFKGHMVAGYACQVDFSP
Retrocopy IPVDFKYIAEPSMHSMPAVTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKIFKGHMVAGYACQVDFSP

Parental  DMSYVISGDGNGKLNIWDWKTTKLYSRFKAHDKVCIGAVWHPHETSKVITCGW-DGLIKLWD
          DMSYVISGDGNGKLNIWDWKTTKLYS.FKAHDKVCIGAVWHP.ETSKVITC.W..GLIKLWD
Retrocopy DMSYVISGDGNGKLNIWDWKTTKLYSQFKAHDKVCIGAVWHPQETSKVITCSW<GGLIKLWD

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	0.06 RPM	16.72 RPM
SRP017611_kidney	1.01 RPM	19.46 RPM
SRP017611_liver	0.08 RPM	5.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1587 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1587 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1587 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000000123	1 retrocopy	retro_dord_8,
Oryctolagus cuniculus	ENSOCUG00000001223	1 retrocopy	retro_ocun_1587 ,