RetrogeneDB ID: retro_ocun_50

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:4025889..4027416(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025363
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021494
• Aliases: None
• Description: None

Sequence

>retro_ocun_50
ATGTACCGAGCACTCCGGGTCTTCGCGCGGTCAGGCCGCCTTGCGCGAGCTCCAGCCTCCGCCTCGGCTCTGGGCTTGAG
TGGCGCTGCTGTCCTCCCAGTCTGGCTTCCGAACGCCGCTCGAATGGCAAGCCAAAATTCCTTCAGGACAGAATATGATA
CCTTTGGGGAACTCAAGGTCCCAAATGATAAGTATTATGGTGCCCAGACTGTGAGATCTACAATGAACTTCAAGATTGGA
GGTGTGACGGAACGCATGCCAATTCCAGTTATTAAAGCTTTTGGCATCTTGAAGCGAGCAGCTGCTGAAGTAAACCAGGA
TTATGGTCTTGATCCAAAGATCGCCAATGCAATAATGAAGGTAGCAGATGAGGTAGCTGAAGGTAAATTAAATGATCATT
TTCCTCTCGTGATATGGCAGACTGGATCGGGAACTCAGACAAATATGAATGTAAATGAAGTCATTAGCAACAGAGCAATT
GAGATGTTGGGAGGTGAACTTGGCAGTAAGAAACCTGTGCATCCCAATGATCATGTTAATAAAAGCCAGAGTTCAAATGA
TACTTTCCCCACAGCAATGCACATTGCTGCTGCAATAGAAGTTCATGAAGTACTCTTACCAGGACTCCAGAAGTTACATG
ATGCTCTGGAAGCAAAATCCAAAGAGTTCGCTCAGATCATCAAAATTGGACGAACTCATACTCAGGATGCTGCTCCGCTT
ACTCTTGGTCAGGAATTCAGTGGTTATGTTCAACAAGTGAAATATGCAATGGCGAGAATAAAAGCCGCCATGCCAAGAAT
CTATGAGCTCGCAGCTGGAGGCACTGCTGTTGGTACTGGCTTAAATACTAGAATTGGCTTTGCAGAAAAGGTTGCTGCGA
AGGTGGCTGCCCTCACAGGCTTGCCTTTTGTCACTGCTCCAAATAAATTTGAAGCTCTGGCTGCTCATGATGCTCTGGTT
GAGCTCAGTGGAGCCATGAACACGACTGCTTGCAGTCTGATGAAGATAGCAAATGATGTTCGTTTTCTGGGTTCTGGCCC
TCGGTCAGGCCTGGGAGAATTGATCTTGCCTGAAAATGAACCGGGAAGCAGTATCATGCCAGGCAAGGTGAACCCTACTC
AGTGTGAAGCAATGACCATGGTTGCAGCCCAGGTCATGGGGAATCATGTTGCTGTTGCAGTTGGAGGCAGCAATGGACAT
TTTGAGCTGAATGTTTTCAAGCCAATGATGATTAAAAATGTGTTGCACTCAGCCAGACTGCTAGGGGATGCTTCAGTTTC
CTTCACAGAAAACTGTGTCCTGGGGATCCAGGCTAACACAGAAAGGATCAATAAGCTAATGAATGAGTCTCTAATGTTGG
TGACAGCTCTCAATCCATATATAGGATATGACAAGGCAGCAAAGATTGCTAAGACAGCGCACAAAAATGGATCAACCTTG
AAAGAAACTGCTATTGAACTTGGGTATCTCACAGCAGAGCAGTTTGATGAGTGGGTGAAACCTAAAGACATGCTGGGTCC
GAAGTGA

Alignment

ORF - retro_ocun_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.78 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASQNSFRTEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTERMPIPVIKAFGILKRAAAEVNQDYGLDP
          ASQNSFRTEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTERMPIPVIKAFGILKRAAAEVNQDYGLDP
Retrocopy ASQNSFRTEYDTFGELKVPNDKYYGAQTVRSTMNFKIGGVTERMPIPVIKAFGILKRAAAEVNQDYGLDP

Parental  KIANAIMKAADEVAEGKLNDHFPLVIWQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKS
          KIANAIMK.ADEVAEGKLNDHFPLVIWQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKS
Retrocopy KIANAIMKVADEVAEGKLNDHFPLVIWQTGSGTQTNMNVNEVISNRAIEMLGGELGSKKPVHPNDHVNKS

Parental  QSSNDTFPTAMHIAAAIEVHEVLLPGLQKLHDALEAKSKEFAQIIKIGRTHTQDAVPLTLGQEFSGYVQQ
          QSSNDTFPTAMHIAAAIEVHEVLLPGLQKLHDALEAKSKEFAQIIKIGRTHTQDA.PLTLGQEFSGYVQQ
Retrocopy QSSNDTFPTAMHIAAAIEVHEVLLPGLQKLHDALEAKSKEFAQIIKIGRTHTQDAAPLTLGQEFSGYVQQ

Parental  VKYAMARIKAAMPRIYELAAGGTAVGTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVEL
          VKYAMARIKAAMPRIYELAAGGTAVGTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVEL
Retrocopy VKYAMARIKAAMPRIYELAAGGTAVGTGLNTRIGFAEKVAAKVAALTGLPFVTAPNKFEALAAHDALVEL

Parental  SGAMNTTACSLMKIANDVRFLGSGPRSGLGELILRHDSVTGDFLEGKVNPTQCEAMTMVAAQVMGNHVAV
          SGAMNTTACSLMKIANDVRFLGSGPRSGLGELIL...........GKVNPTQCEAMTMVAAQVMGNHVAV
Retrocopy SGAMNTTACSLMKIANDVRFLGSGPRSGLGELILPENEPGSSIMPGKVNPTQCEAMTMVAAQVMGNHVAV

Parental  TVGGSNGHFELNVFKPMMIKNVLHSARLLGDASVSFTENCVLGIQANTERINKLMNESLMLVTALNPHIG
          .VGGSNGHFELNVFKPMMIKNVLHSARLLGDASVSFTENCVLGIQANTERINKLMNESLMLVTALNP.IG
Retrocopy AVGGSNGHFELNVFKPMMIKNVLHSARLLGDASVSFTENCVLGIQANTERINKLMNESLMLVTALNPYIG

Parental  YDKAAKIAKTAHKNGSTLKETAIELGYLTAEQFDEWVKPKDMLGPK
          YDKAAKIAKTAHKNGSTLKETAIELGYLTAEQFDEWVKPKDMLGPK
Retrocopy YDKAAKIAKTAHKNGSTLKETAIELGYLTAEQFDEWVKPKDMLGPK

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	0.06 RPM	13.69 RPM
SRP017611_kidney	0.00 RPM	51.69 RPM
SRP017611_liver	0.08 RPM	15.57 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_50 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_50 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017359	1 retrocopy	retro_cjac_2339,
Echinops telfairi	ENSETEG00000018721	2 retrocopies	retro_etel_1069, retro_etel_1457,
Microcebus murinus	ENSMICG00000003451	2 retrocopies	retro_mmur_1215, retro_mmur_720,
Mus musculus	ENSMUSG00000026526	1 retrocopy	retro_mmus_3600,
Oryctolagus cuniculus	ENSOCUG00000021494	1 retrocopy	retro_ocun_50 ,
Otolemur garnettii	ENSOGAG00000009936	1 retrocopy	retro_ogar_322,
Rattus norvegicus	ENSRNOG00000003653	1 retrocopy	retro_rnor_2979,
Xenopus tropicalis	ENSXETG00000032112	1 retrocopy	retro_xtro_55,