RetrogeneDB ID: retro_ocun_216

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018770:105256..106348(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027867
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000026002
• Aliases: None
• Description: None

Sequence

>retro_ocun_216
ATGGCCTCTAAATCTTGGCTGAATTTTTTAGTCTTTCTCTGTGGATCAGCAATAGGATTTTTTTTATGTTCTCAACTGTT
TAGTATTTTGCTGGGAGAACACAGTGACACCCAGCCTAACATTCTTCATAATGACCCTCATGCTAGGCATTCAGATGATA
ATGGACAGAATCATCTAGAAGGACAAATGAACTTCAATGCAGATTCCAGCCAACATAAAGATGAGAACACAGACATCGCT
GAAAACCTCTATCAGAAAGTTAAAATTCTTTGCTGGGTTATGACAGGCCCTCAAAATCTAGAGAAAAAGGCCAGACACGT
CAAAGTAACATGGGCCCAGCGTTGTAATAAAGTGCTGTTTATGAGTTCAGAAGAAAATAAAGACTTCCCTACCGTGGGAT
TAAAAACCAAAGAAGGCAGAGATCAGCTATACTGGAAAACAATTAAAGCTTTTCAGTATGTTCATGACCATTATTTAGAA
GATGCCGATTGGTTTCTGAAAGCTGATGATGATACATATGTCATACTGGACAACTTGAGATGGCTTCTTTCAAAATATGA
CCCTGAAGAACCCATTTACTTCGGGAGAAGATTTAAGCCCTATGTAAAGCAGGGCTACATGAGTGGAGGAGCGGGATATG
TACTAAGCAAAGAAGCCCTACGGAGATTTGTTGATGCATTCAAAACAGACAAATGTACACATAGTTCCTCCATTGAAGAC
TTAGCGCTGGGAAGATGCATGGAAATTATAAATGTCCAAGCAGGAGATTCCAGAGACACCACTGGAAAAGAAACTTTTCA
TCCCTTTGTACCGGAACACCACTTAATCAAAGGTTATCTCCCCAGAACCTTTTGGTACTGGAATTATAACTATTATCCTC
CTATAGAGGGTCCAGGTTGCTGTTCTGATCTTGCAGTTTCTTTTCATTATGTTGATTCTACAACTATGTATGAATTAGAA
TACCTCGTTTATCATCTTCGTCCATATGGTTATTTATACAGATACCAACCTGAATTACCTGAAAATATATTAAAGGAAAT
AAGTCAAGCAAACAAAAATGAAGATTCAAAAGTAAAATTAGGAAACCCTTGA

Alignment

ORF - retro_ocun_216 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MASKSWLNFLVFLCGSAIGFFLCSQLFSILLGEHSDTQPNILHNDPHARHSDDNGQNHLEGQMNFNADSS
          MASKSWLNFLVFLCGSAIGFFLCSQLFSILLGEHSDTQPNILHNDPHARHSDDNGQNHLEGQMNFNADSS
Retrocopy MASKSWLNFLVFLCGSAIGFFLCSQLFSILLGEHSDTQPNILHNDPHARHSDDNGQNHLEGQMNFNADSS

Parental  QHKDENTDIAENLYQKVKILCWVMTGPQNLEKKARHVKVTWAQRCNKVLFMSSEENKDFPTVGLKTKEGR
          QHKDENTDIAENLYQKVKILCWVMTGPQNLEKKARHVKVTWAQRCNKVLFMSSEENKDFPTVGLKTKEGR
Retrocopy QHKDENTDIAENLYQKVKILCWVMTGPQNLEKKARHVKVTWAQRCNKVLFMSSEENKDFPTVGLKTKEGR

Parental  DQLYWKTIKAFQYVHDHYLEDADWFLKADDDTYVILDNLRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGG
          DQLYWKTIKAFQYVHDHYLEDADWFLKADDDTYVILDNLRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGG
Retrocopy DQLYWKTIKAFQYVHDHYLEDADWFLKADDDTYVILDNLRWLLSKYDPEEPIYFGRRFKPYVKQGYMSGG

Parental  AGYVLSKEALRRFVDAFKTDKCTHSSSIEDLALGRCMEIINVQAGDSRDTTGKETFHPFVPEHHLIKGYL
          AGYVLSKEALRRFVDAFKTDKCTHSSSIEDLALGRCMEIINVQAGDSRDTTGKETFHPFVPEHHLIKGYL
Retrocopy AGYVLSKEALRRFVDAFKTDKCTHSSSIEDLALGRCMEIINVQAGDSRDTTGKETFHPFVPEHHLIKGYL

Parental  PRTFWYWNYNYYPPIEGPGCCSDLAVSFHYVDSTTMYELEYLVYHLRPYGYLYRYQPELPENILKEISQA
          PRTFWYWNYNYYPPIEGPGCCSDLAVSFHYVDSTTMYELEYLVYHLRPYGYLYRYQPELPENILKEISQA
Retrocopy PRTFWYWNYNYYPPIEGPGCCSDLAVSFHYVDSTTMYELEYLVYHLRPYGYLYRYQPELPENILKEISQA

Parental  NKNEDSKVKLGNP
          NKNEDSKVKLGNP
Retrocopy NKNEDSKVKLGNP

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	1.05 RPM
SRP017611_kidney	0.30 RPM	2.64 RPM
SRP017611_liver	0.23 RPM	1.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_216 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_216 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_216 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000225	2 retrocopies	retro_chof_1782, retro_chof_2581,
Dasypus novemcinctus	ENSDNOG00000017353	2 retrocopies	retro_dnov_1801, retro_dnov_1905,
Homo sapiens	ENSG00000106392	2 retrocopies	retro_hsap_3177, retro_hsap_4065,
Loxodonta africana	ENSLAFG00000000063	1 retrocopy	retro_lafr_1166,
Myotis lucifugus	ENSMLUG00000014789	1 retrocopy	retro_mluc_1310,
Macaca mulatta	ENSMMUG00000016338	1 retrocopy	retro_mmul_2009,
Oryctolagus cuniculus	ENSOCUG00000026002	1 retrocopy	retro_ocun_216 ,
Otolemur garnettii	ENSOGAG00000012847	1 retrocopy	retro_ogar_855,
Petromyzon marinus	ENSPMAG00000001562	1 retrocopy	retro_pmar_2,
Pan troglodytes	ENSPTRG00000018925	2 retrocopies	retro_ptro_2266, retro_ptro_2755,