RetrogeneDB ID: retro_ocun_927

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:81791170..81791611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CD302
• Ensembl ID: ENSOCUG00000016361
• Aliases: None
• Description: CD302 molecule [Source:HGNC Symbol;Acc:30843]

Sequence

>retro_ocun_927
CTGATAAGCATATATAATGGAGAAGAAAATGCTTATATACTAGATACTTTGAAAAAGCAATGGTAAAGCCCAGATGATAT
CCTACTAGGCATGTTTTATGACACAGCTGATGCGAATTTCAAGTGGTTTGACGATTCAGATACGACATTTGATAAATAGG
CAGCCAAAGACGATGGCGAGGATCTAGTTGACACCTGTGGTTTTCTGCACACCAAGACAGGTGAATGGAAAAACGGGAAT
TTTGAAGTTTCTTCTGTGGAAGGAACACTTTATAAAGCAGCTGTACCATATGAAAAGAAGTATTTATCAGATGACCACAT
TTTAATATCAGCTTTGGTGACTGCTAGCACAGTAATTTTGACAGTTTTTGGAGCAATCATTTGTTTCCTGTACAAAAGAA
GTTCTGAATCTGGTTTCAGCAGCTTTTTCAATGGCACCCCA

Alignment

ORF - retro_ocun_927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 63.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MISIHNEEENAFILDTLKKQWKGPDDILLGMFYDTDDASFKWFDNSDMTFDKWAAQDDSEDLVDTCGFLH
          .ISI.N.EENA.ILDTLKKQW..PDDILLGMFYDT.DA.FKWFD.SD.TFDK.AA.DD.EDLVDTCGFLH
Retrocopy LISIYNGEENAYILDTLKKQW*SPDDILLGMFYDTADANFKWFDDSDTTFDK*AAKDDGEDLVDTCGFLH

Parental  TKTGEWKKGNCEVSSVEGTLCKAAVPFEKKYLSDDHILISALVTASTVILTVFGAIIWFLYKRSSEFGFT
          TKTGEWK.GN.EVSSVEGTL.KAAVP.EKKYLSDDHILISALVTASTVILTVFGAII.FLYKRSSE.GF.
Retrocopy TKTGEWKNGNFEVSSVEGTLYKAAVPYEKKYLSDDHILISALVTASTVILTVFGAIICFLYKRSSESGFS

Parental  TVFSTAP
          ..F...P
Retrocopy SFFNGTP

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	0.11 RPM	6.24 RPM
SRP017611_kidney	0.00 RPM	38.41 RPM
SRP017611_liver	0.00 RPM	45.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_927 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_927 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007947	2 retrocopies	retro_chof_224, retro_chof_2460,
Oryctolagus cuniculus	ENSOCUG00000016361	1 retrocopy	retro_ocun_927 ,
Tarsius syrichta	ENSTSYG00000002564	1 retrocopy	retro_tsyr_71,