RetrogeneDB ID: retro_ocun_74

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019037:85693..86506(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000020938
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_ocun_74
ATGTCAGTGAATCAGCAATCTCTAGATTCAGATAGTACAACAGATGTGGAAGTCATTACAGATACTGAAGAAGAACTTAT
TAAAGAATGTGAAGAAATGTGGAAAGAAATGGAAGAATGTCAGAATAAATTATTGCTTATTGGAACTGAGACACTCACTG
ATTCAAATGCTCAGCTTTCACTATTAATTATGCAAGTGAAATGTTTGACTGCCGAACTGTCAGTGCAAAAAGAAACACCT
GAAATAGCTCCCCTAAATGACGGTGTTCTGGTAACATTAGGAAAAGAAGAGTTCCAAAAATTGCAGCATGATCTTGAAAT
GGTGCTATCTACTATTCAGTCAAAGAATGAAAAGTTAAAGGAAGACTTAAAAAGAGAGCAGCAGTGGTTGGAGGAACAGC
AACAGATAATGGAATCTCTTAATGTACTACACAGTGAATTGAAAAATCAGGTTGTGACATTTTCTGAATCAAGAATCTTT
ACTGAGCTGAAAACTAAAATGCTTAATGTAAAAAAATATAAGAAGAAACTCTTGATTACCTTGGGTGAGTTTCTAGAAGA
CCACTTTCCTTTGCCTGATGGAAGTGTTAAAAAGAAAAAGAAAAGCACTCAAGAATCAACTGCACAGCTGATAACACTAC
ATGAAATATTAGAGACTCTTATAAATAGATTCTTTGATGTTTTGCATGATCCATATGTCAAAATTAGTGATTCCTTTTGC
CCTCCTTATATTGAACTGCTGCTGTGTAATGGAATTGCCTTGAGACATCCAGAAGACCCAACCCAAATAAGATTAGAAGC
CTTCCTTCAGTAA

Alignment

ORF - retro_ocun_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVNQQSLDPDSTTDVEVVTDTEEELIKECEEMWKEMEEIKCQNKLSLIGTETLTDSNAQISLLIMQVKC
          MSVNQQSLD.DSTTDVEV.TDTEEELIKECEEMWKEMEE..CQNKL.LIGTETLTDSNAQ.SLLIMQVKC
Retrocopy MSVNQQSLDSDSTTDVEVITDTEEELIKECEEMWKEMEE--CQNKLLLIGTETLTDSNAQLSLLIMQVKC

Parental  LTAELSQWQKETPEIAPLNDDVLVTLGKEEFQKLQHDLEMVLSTIQSKNEKLKEDLKREQQWLDEQQQIM
          LTAELS..QKETPEIAPLND.VLVTLGKEEFQKLQHDLEMVLSTIQSKNEKLKEDLKREQQWL.EQQQIM
Retrocopy LTAELSV-QKETPEIAPLNDGVLVTLGKEEFQKLQHDLEMVLSTIQSKNEKLKEDLKREQQWLEEQQQIM

Parental  ESLNVLHSELKNQVVTFSESRIFTELKTKLLNVKKYKKKLLITLGEFLEDHFPLPDGSVKKKKKSIQEST
          ESLNVLHSELKNQVVTFSESRIFTELKTK.LNVKKYKKKLLITLGEFLEDHFPLPDGSVKKKKKS.QEST
Retrocopy ESLNVLHSELKNQVVTFSESRIFTELKTKMLNVKKYKKKLLITLGEFLEDHFPLPDGSVKKKKKSTQEST

Parental  AQLITLHEILETLINRLFDVPHDPYVKISDSFWPPYIELLLRNGIALRHPEDPTQIRLEAFHQ
          AQLITLHEILETLINR.FDV.HDPYVKISDSF.PPYIELLL.NGIALRHPEDPTQIRLEAF.Q
Retrocopy AQLITLHEILETLINRFFDVLHDPYVKISDSFCPPYIELLLCNGIALRHPEDPTQIRLEAFLQ

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_74 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_74 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_74 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,