RetrogeneDB ID: retro_ocun_1206

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:107117826..107118464(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027627
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCH1
• Ensembl ID: ENSOCUG00000003060
• Aliases: None
• Description: GTP cyclohydrolase 1 [Source:HGNC Symbol;Acc:4193]

Sequence

>retro_ocun_1206
ATGGAGAAGGGCCCAGTGCCTGCGCTGGCAGAGACGCTGGGGGCGACCGGTGCAGCAACGGGTTCCCCGAGTGGGACCCG
CCGCAGCTCGGACCCAGCTGGCCGGCGGGGAAGCCCCCGCAGCCCGAGGCCAGAGGAGCGCCAGCTGCGGACGGCTGGAA
GGGCGAGCTGCTGCGCAGCGAGGAGGATAATGAGCTGAACCTCCCCTACCTGGCGGCCGCCTACGCGTCCATCCTGCGCT
TGCTGGGCAAGGACCCGCAGCGCCAGGGGCTGCTCAAGACGCCCTGGAGGGCGGCCACGGCCATGCAGTTCTTCACCAAG
GGCTACCAGGAGACCATCTCGGATGTCCTCAACGATGCTATCTTTGATGAAGATCACGACGAGATGGTGATTGTGAAGGA
CATAGACATGTTTTCCATGTGTGAGCATCATCTGGTTCCATTTGTGGGAAAGGTGCATATCGGTTATCTTCCTAACAAGC
AAATCCTTGGCCTCAGCAAACTTGCCGGGATTGTAGAAATCTACAGTAGAAGACTACAAGTTCAAGAGCGCCTTACGAAG
CAAATCGCTGTGGCGATCACGGAAGCCTTGCACCCTGCTGGAGTTGGGGTGGTGGTTGAAGCAACACACATGTGCATG

Alignment

ORF - retro_ocun_1206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.19 %
• Parental protein coverage: 85.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEKGPVRALAET-PRGARCSNGFPEREPPRPGPSRPAEKPPRPEAGGAPTADGWKGERPRSEEDNELNLP
          MEKGPV.ALAET...G.RCSNGFPE..PP..GPS.PA.KPP.PEA.GAP.ADGWKGE..RSEEDNELNLP
Retrocopy MEKGPVPALAET<AGGDRCSNGFPEWDPPQLGPSWPAGKPPQPEARGAPAADGWKGELLRSEEDNELNLP

Parental  NLAAAYASILRSLGEDPQRQGLLKTPWRAATAMQFFTKGYQETISDVLNDAIFDEDHDEMVIVKDIDMFS
          .LAAAYASILR.LG.DPQRQGLLKTPWRAATAMQFFTKGYQETISDVLNDAIFDEDHDEMVIVKDIDMFS
Retrocopy YLAAAYASILRLLGKDPQRQGLLKTPWRAATAMQFFTKGYQETISDVLNDAIFDEDHDEMVIVKDIDMFS

Parental  MCEHHLVPFVGKVHIGYLPNKQVLGLSKLARIVEIYSRRLQVQERLTKQIAVAITEALHPAGVGVVVEAT
          MCEHHLVPFVGKVHIGYLPNKQ.LGLSKLA.IVEIYSRRLQVQERLTKQIAVAITEALHPAGVGVVVEAT
Retrocopy MCEHHLVPFVGKVHIGYLPNKQILGLSKLAGIVEIYSRRLQVQERLTKQIAVAITEALHPAGVGVVVEAT

Parental  HMCM
          HMCM
Retrocopy HMCM

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	0.72 RPM
SRP017611_kidney	0.00 RPM	0.61 RPM
SRP017611_liver	0.15 RPM	28.52 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1206 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1206 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000003060	1 retrocopy	retro_ocun_1206 ,
Ictidomys tridecemlineatus	ENSSTOG00000020010	2 retrocopies	retro_itri_739, retro_itri_92,