RetrogeneDB ID: retro_ocun_1237

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:70149892..70150684(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027992
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000024818
• Aliases: None
• Description: None

Sequence

>retro_ocun_1237
AAAGAATTTGCGGATGATGGTGTCAAATATCTGGAACTAAGGAGCACTCCCAGAAGAGAAAATGCTACTGGAATGACTAA
AAAGAGTTATGTGGAATCTATACTTGAGGGTATAAAACAGTCCAAACAAGAAAACTCAGACATTGATGTTAGGTATTTGA
TAGCAATCGAAAGAAGAGGCGGCCCTTCAGTTGCCAAGGAGACCGTTAAACTTGCGGAGGAGTTCTTCCTTTCTACTCAG
GATGTAGTTCTTGACCTTGACCTTAGTGGAGACCCTACTATAGGACGAGCAGAAGACTTCTTGGAACCTCTTTTAGAAGC
TAAAAATGCAGGTCTGAAGTTGGCATTGCGTCTTTCAGAGATCCCAAACCAAGGAAAAGAAACCCAAATGCTCTTGGATC
TACTTCCTGACAGAACTGGCATGGGACTTTCCTCAACTCTTCTGAGGGAGGATCCCTGGATCTGGTGGACTTTGTGAGGC
AACATTGGATACCTCTGGAACTGTGTTTGACCTCAAACATCAAAAGTCAGACAGTTCCATCTTATGACCAGCATCATTTC
GGATTCTGGTGCAGCATTGTACATCCTTCTGTGATCTGTACCGATGATAAAGGTGTTTTTTGCAACATACCTTTCTCAAG
AGTACCGGCTGGCAGCTGAAACATTTAATTTGACCCAGTCTCAGGTGTGGGATTTATCGCATGAATCCATCAACTACATC
TTTGCTTCTGATAGCACCAGATCTGAACTGAGGAAGAAGTGGAATCATCTGAAGCCCAAAGTGCTACAATTT

Alignment

ORF - retro_ocun_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 74.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEFADDGVKYLELRSTPRRENATGMTKKSYVESILEGIKQAKQENLDIDVRYLIAIDRRGGPSVAKETVK
          KEFADDGVKYLELRSTPRRENATGMTKKSYVESILEGIKQ.KQEN.DIDVRYLIAI.RRGGPSVAKETVK
Retrocopy KEFADDGVKYLELRSTPRRENATGMTKKSYVESILEGIKQSKQENSDIDVRYLIAIERRGGPSVAKETVK

Parental  LAEEFFLSTEDVVLGLDLSGDPTIGQAEDFLEPLLEAKNAGLKLALHLSEIPNQGKETQMLLDLLPDRIG
          LAEEFFLST.DVVL.LDLSGDPTIG.AEDFLEPLLEAKNAGLKLAL.LSEIPNQGKETQMLLDLLPDR.G
Retrocopy LAEEFFLSTQDVVLDLDLSGDPTIGRAEDFLEPLLEAKNAGLKLALRLSEIPNQGKETQMLLDLLPDRTG

Parental  -HGTFLNSSEGGSLDLVDFVRQHRIPLELCLTSNIKSQTVPSYDQHHFGFWYSIAHPSVICTDDKGV-FA
          .HGTFLNSSEGGSLDLVDFVRQH.IPLELCLTSNIKSQTVPSYDQHHFGFW.SI.HPSVICTDDKGV.FA
Retrocopy <HGTFLNSSEGGSLDLVDFVRQHWIPLELCLTSNIKSQTVPSYDQHHFGFWCSIVHPSVICTDDKGV>FA

Parental  TYLSQEYRLAAETFNLTQSQVWDLSYESINYIFASDSTRSELRKKWNHLKPKVLQF
          TYLSQEYRLAAETFNLTQSQVWDLS.ESINYIFASDSTRSELRKKWNHLKPKVLQF
Retrocopy TYLSQEYRLAAETFNLTQSQVWDLSHESINYIFASDSTRSELRKKWNHLKPKVLQF

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	3.37 RPM
SRP017611_kidney	0.00 RPM	2.94 RPM
SRP017611_liver	0.00 RPM	0.92 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1237 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1237 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1237 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014476	1 retrocopy	retro_btau_1539,
Cavia porcellus	ENSCPOG00000002337	1 retrocopy	retro_cpor_1193,
Oryctolagus cuniculus	ENSOCUG00000024818	2 retrocopies	retro_ocun_1237 , retro_ocun_85,
Sus scrofa	ENSSSCG00000004710	1 retrocopy	retro_sscr_530,