RetrogeneDB ID: retro_ocun_1199

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:86394492..86394965(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011568
• Aliases: None
• Description: None

Sequence

>retro_ocun_1199
TTGTCAGTGAATCAGCAAGATCTAGATCCAGAGAGTGCCATAGATGTGGAAGTTGTTACAGGTACTGAAGAATAACTTAT
TAAAGAATGTGAAGAAATGTGAAAAGATATGGAAGGATGTCAGAATAAATGATCGCTCATTAGAGCTGAGACATTCACTG
ATTCAAATGCTCAGCTTTCACTATAATTATGAAATGTTTGACCGCTGGACTCAGTCACTGGCACAAAGAAACACCTGAAA
TAGCTCCCCTCAGTGAAGATGTTCTGGTAACACTGGGAAAAGAGTTCCAAAAACCGCAGCATGATCTTGAGATAGTGCCA
TCTACTATTCAGGCAAAGAATGAAAAGTTAAAGGAAGACTTCCAAAGAGAGCAACAGTGCTTGGATGACTAGCAACAGAT
AATGGAATCTCTTAATGTACTACACAGTGAACTGAAAAATCAGGTTGTGGCATTTTCTAAATCAAGAATCTTT

Alignment

ORF - retro_ocun_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 59.71 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSVNQQSLDPDSTTDVEVVTDTEEELIKECEEMWKEMEEIKCQNKLSLIGTETLTDSNAQISL-LIMQVK
          .SVNQQ.LDP.S..DVEVVT.TEE.LIKECEEM.K.ME...CQNK.SLI..ET.TDSNAQ.SL..IM..K
Retrocopy LSVNQQDLDPESAIDVEVVTGTEE*LIKECEEM*KDMEG--CQNK*SLIRAETFTDSNAQLSL<IIM--K

Parental  CLTAELSQWQKETPEIAPLNDDVLVTLGKEEFQKLQHDLEMVLSTIQSKNEKLKEDLKREQQWLDEQQQI
          CLTA.LS.W.KETPEIAPL..DVLVTLGKE.FQK.QHDLE.V.STIQ.KNEKLKED..REQQ.LD..QQI
Retrocopy CLTAGLSHWHKETPEIAPLSEDVLVTLGKE-FQKPQHDLEIVPSTIQAKNEKLKEDFQREQQCLDD*QQI

Parental  MESLNVLHSELKNQVVTFSESRIF
          MESLNVLHSELKNQVV.FS.SRIF
Retrocopy MESLNVLHSELKNQVVAFSKSRIF

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	0.94 RPM
SRP017611_kidney	0.00 RPM	0.51 RPM
SRP017611_liver	0.00 RPM	0.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1199 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1199 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013993	1 retrocopy	retro_chof_1252,
Dipodomys ordii	ENSDORG00000007357	1 retrocopy	retro_dord_787,
Equus caballus	ENSECAG00000019165	1 retrocopy	retro_ecab_181,
Erinaceus europaeus	ENSEEUG00000005831	1 retrocopy	retro_eeur_81,
Monodelphis domestica	ENSMODG00000019645	1 retrocopy	retro_mdom_1446,
Oryctolagus cuniculus	ENSOCUG00000011568	2 retrocopies	retro_ocun_1199 , retro_ocun_74,
Tursiops truncatus	ENSTTRG00000006527	1 retrocopy	retro_ttru_1310,