RetrogeneDB ID: retro_ocun_307

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:133849977..133851129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD2AP
• Ensembl ID: ENSOCUG00000005026
• Aliases: None
• Description: CD2-associated protein [Source:HGNC Symbol;Acc:14258]

Sequence

>retro_ocun_307
AAAACTCAAAGTGTAGAGATAAAAACAGATACTGAAGGTAAAATAAAAGCAAAGGAATATTGTAGAACATTATTTGCCTA
TGAAGGTACTAATGAAGATGAACTTACATTTAAAGAGGGGGAGATAATCCATTTGATAAGTAAGGAGACTGGAGAAACTG
GCTGGTGGAAAGGTGAACTTAATGGTAAAGAAGGAGTATTTCCAGACAATTTTGCTGTTCAAATAAGTGAATTGGATAAA
GATTTCCCAAAACCAAAGAAACCACCACCTCCTATTAAGGGTCCAGCTCCAAAGCCTGACTTGATTGCTGCGGAGAAGAA
GTATTTTCTGTTAAAGCCTGAAGAAAAAGATGAAAAATCAGTGCTGGAACAAAAACCTTCTAAACCAGCTGCTCCACAAG
TCCCACCCAAGAAACCCACTCCACCCACCAAAGCCAATAATATATTGAGATCCTCTGGAACAACGTACCCAAAGCGACCT
GAAAAACCAGTTCCCCCACCACCTCCTATAGCCAAGATTAATGGGGAAGTTTCTATCATTTCATCAAAGTTTGAAACTGA
GCCCGTATCAAAACCAAAGTTAGATTCTGAACAGTTGCCACTTAGACCAAAATCAGTAGACCTTGACTCATTTACAGTAA
GGAGCTCTAAAGAAACAGATGTTGTAAATTTTGATGACATAGCTTCCTCAGAAAACTTGCTACATCTCACAGCAAATAGA
CCTAAGATGCCTGGAAGAAGGCTGCCTGGCCGCTTCAATGGTGGACATTCTCCAACTCAGAGCCCAGAGAAAAATTTGAA
GTTACCAAAGGAAGAAGATAGTGCCAATGTAAAGCCATCTGAATTGAAAAAGGATACATCCTACTCTCCAAAGCCATCTG
TGTATACAACTTCAAGTGCATCTAAAGCAAATTCAGCTGCATTCTTAACTCCATTAGAAACCAAAGCTAAACTAGAGGCA
GATGATGGGAAAAAAAATTCCCTGGATGAACTCAGAGCCCAGATTATTGAATTGCTGTGTATTGTAGAAGCGCTAAAGAA
GGATCATGGGAAAGAACTGGAAAAACTGAGAAAAGATTTGGAAGAAGAGAAGGCTCTTAGGAGTAATCTAGAGATGGAAA
TAGAGAAGCTGAAGAAAGCTGTCCTGTCTTCT

Alignment

ORF - retro_ocun_307 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.71 %
• Parental protein coverage: 60.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTPSVEIKTDTEGKIKAKEYCRTLFAYEGTNEDELTFKEGEIIHLISKETGETGWWKGELNGKEGVFPDN
          KT.SVEIKTDTEGKIKAKEYCRTLFAYEGTNEDELTFKEGEIIHLISKETGETGWWKGELNGKEGVFPDN
Retrocopy KTQSVEIKTDTEGKIKAKEYCRTLFAYEGTNEDELTFKEGEIIHLISKETGETGWWKGELNGKEGVFPDN

Parental  FAVQISELDKDFPKPKKPPPPIKGPAPKPDLIAAEKKYFLLKPEEKESSDEKSVLEQKPSKPAAPQVPPK
          FAVQISELDKDFPKPKKPPPPIKGPAPKPDLIAAEKKYFLLKPEEK...DEKSVLEQKPSKPAAPQVPPK
Retrocopy FAVQISELDKDFPKPKKPPPPIKGPAPKPDLIAAEKKYFLLKPEEK---DEKSVLEQKPSKPAAPQVPPK

Parental  KPTPPTKANNILRSSGTTYPKRPEKPVPPPPPIAKINGEVSIISSKFETEPVSKPKLDSEQLPLRPKSVD
          KPTPPTKANNILRSSGTTYPKRPEKPVPPPPPIAKINGEVSIISSKFETEPVSKPKLDSEQLPLRPKSVD
Retrocopy KPTPPTKANNILRSSGTTYPKRPEKPVPPPPPIAKINGEVSIISSKFETEPVSKPKLDSEQLPLRPKSVD

Parental  LDSFTVRSSKETDVVNFDDIASSENLLHLTANRPKMPGRRLPGRFNGGHSPTQSPEKNLKLPKEEDSANV
          LDSFTVRSSKETDVVNFDDIASSENLLHLTANRPKMPGRRLPGRFNGGHSPTQSPEKNLKLPKEEDSANV
Retrocopy LDSFTVRSSKETDVVNFDDIASSENLLHLTANRPKMPGRRLPGRFNGGHSPTQSPEKNLKLPKEEDSANV

Parental  KPSELKKDTSYSPKPSVYTTSSASKANSAAFLTPLETKAKLEADDGKKNSLDELRAQIIELLCIVEALKK
          KPSELKKDTSYSPKPSVYTTSSASKANSAAFLTPLETKAKLEADDGKKNSLDELRAQIIELLCIVEALKK
Retrocopy KPSELKKDTSYSPKPSVYTTSSASKANSAAFLTPLETKAKLEADDGKKNSLDELRAQIIELLCIVEALKK

Parental  DHGKELEKLRKDLEEEKALRSNLEMEIEKLKKTVLSS
          DHGKELEKLRKDLEEEKALRSNLEMEIEKLKK.VLSS
Retrocopy DHGKELEKLRKDLEEEKALRSNLEMEIEKLKKAVLSS

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	0.22 RPM	4.53 RPM
SRP017611_kidney	3.04 RPM	28.18 RPM
SRP017611_liver	1.16 RPM	6.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_307 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_307 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009776	1 retrocopy	retro_mluc_2422,
Mus musculus	ENSMUSG00000061665	1 retrocopy	retro_mmus_1604,
Oryctolagus cuniculus	ENSOCUG00000005026	1 retrocopy	retro_ocun_307 ,
Rattus norvegicus	ENSRNOG00000011987	1 retrocopy	retro_rnor_2040,