RetrogeneDB ID: retro_ocun_736

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:6664926..6665333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FGF11
• Ensembl ID: ENSOCUG00000004215
• Aliases: None
• Description: fibroblast growth factor 11 [Source:HGNC Symbol;Acc:3667]

Sequence

>retro_ocun_736
AGTGTCCAGGGCATCCCAGAGGGCATCAGCTCCTTCACCCACTCAACCTGATCCCCGTGGGGCTCTGGGCGGTCCCCATC
CAGAGTGCCAAGCTGGGTCACCACGTGGTCATGATGGCCGAGCGGCTGCTCTACAGCTCACCATATTTCACAGCTGAGTG
TCGCTTTTAGGAGTATGTCTTTGAGAACTACTATGTCCTGTACACCTCTGCTCTCTACCGCCAGTGGCATTATGGCCGGG
CCTGGTACCTAGGCCTGGATAAGGAGTGCTGGATCATGAAGGGAAACCGAGTGAATTAGACCAAGGCTGCTGCCCACTTT
GTGTCCAAGCTCCTGGAGCTGGCCATGGACTGAGAACCTTCTCTCCACAGTGTCCCCAGGATGTCCCTGTCCAGTCCCCC
TGCACCT

Alignment

ORF - retro_ocun_736 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 59.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SIQGAPEDTSSFTH-FNLIPVGLRVVTIQSAKLGHYMAMNAEGLLYSSPHFTAECRFKECVFENYYVLYA
          S.QG.PE..SSFTH..NLIPVGL..V.IQSAKLGH...M.AE.LLYSSP.FTAECRF.E.VFENYYVLY.
Retrocopy SVQGIPEGISSFTH<LNLIPVGLWAVPIQSAKLGHHVVMMAERLLYSSPYFTAECRF*EYVFENYYVLYT

Parental  SALYRQRRSGRAWYLGLDKEGRVMKGNRVKKTKAAAHFVPKLLEVAMYREPSLHSVPETSPSSPPAP
          SALYRQ...GRAWYLGLDKE...MKGNRV..TKAAAHFV.KLLE.AM..EPSLHSVP..S.SSPPAP
Retrocopy SALYRQWHYGRAWYLGLDKECWIMKGNRVN*TKAAAHFVSKLLELAMD*EPSLHSVPRMSLSSPPAP

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	7.17 RPM
SRP017611_kidney	0.00 RPM	0.41 RPM
SRP017611_liver	0.00 RPM	0.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_736 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_736 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_736 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
Oryctolagus cuniculus	ENSOCUG00000004215	1 retrocopy	retro_ocun_736 ,
Sarcophilus harrisii	ENSSHAG00000004172	1 retrocopy	retro_shar_117,