RetrogeneDB ID: retro_ocun_1327

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:126264472..126265375(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000021090
• Aliases: None
• Description: None

Sequence

>retro_ocun_1327
GTGCTCACAGGAGTTACTCTGTACAGACATCTTAAAAACTACCTTCTAACTGAAGAACAGTTACATGAAAATAACTACTC
TCGGCCCAACCCTGACAAACCTGGATGTATTCTTTTAAATCCATGCGTGACAAAAACTTCTGTAAACGATGCTTCTAAGA
AGATCTGTTGTCGATGTGGGAAAATCTATGACGTGACTCCCTCAGGCAAACACAGTAGGGTAGAAGAATGTTACTACCAC
TTTGGCCAAGTACGAAGTCATAAAGTCCTTGAAGGCTTAGAATCTCGATATAGCTGTAGTGGAGCAGTTCTTGGATCCCC
TGGGTGTCAGGAGTCCAAGCTTCATGTTCATGACCAAAAAGAAAACCTAGAGGGTTTTGTGAAGACTTCAGTCAAAATCC
CACCAGCTGATGGTAACTATGGCATGTTTGCAGTAAATTGTGAGATGAGCTATACAGTCAAAGGCTTGGAACTTACTTGA
GTGACAGTGGTTGACTCCAGCTTCCAGATGGTCTGTGATACATTTGTGAAACCTGATGAAGAAATCATTGACTATAACAC
TAAGTTTTCTGGTGTGGAGGAAGATGACTTGAGGAACATTAGAACCTCCATCCGTGATGTGCAAGCCGTCTTGCTGAACT
TGTTTAGTGCGGATACCATACTCATTGGACATAGCTTTGAATAAAGTCTGTATGCTCTTAAGCTAATTCACACTTGTGTT
GTGGACACAGCAGTTATGTTTCCTCATCGGCGAGGCCTGCCTCACAAAAGATCCCTTGAGAGTCTAGTGGCTGACTACCT
GCAGAGAATCATTCAGGATGATGGTCACAATACTAGTGAAAAAGAAAAAGCTTGCATGGAGTTGGTCCTTTGGAGAGTAA
AAGAAGACCTGAAAGGAAAGAAG

Alignment

ORF - retro_ocun_1327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.12 %
• Parental protein coverage: 72.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLTGVTLYRHLRNHLLTEEQLRENNYPRPNPDKPGCVLLNPCMTKTSVNDASKKICCRCGKIYDVTPSGK
          .LTGVTLYRHL.N.LLTEEQL.ENNY.RPNPDKPGC.LLNPC.TKTSVNDASKKICCRCGKIYDVTPSGK
Retrocopy VLTGVTLYRHLKNYLLTEEQLHENNYSRPNPDKPGCILLNPCVTKTSVNDASKKICCRCGKIYDVTPSGK

Parental  HSRVEECYYHFGQVRSHKVLDGLESRYSCCGGVLGSPGCQESKLHVHDQKENLEGFVKTSVKIPPADGNY
          HSRVEECYYHFGQVRSHKVL.GLESRYSC.G.VLGSPGCQESKLHVHDQKENLEGFVKTSVKIPPADGNY
Retrocopy HSRVEECYYHFGQVRSHKVLEGLESRYSCSGAVLGSPGCQESKLHVHDQKENLEGFVKTSVKIPPADGNY

Parental  GVFAVNCEMCYTVKGLELTRVTVVDSSFQMVCDTFVKPDEEIIDYNTRFSGVVEDDLKNIRTSIRDVQAI
          G.FAVNCEM.YTVKGLELT.VTVVDSSFQMVCDTFVKPDEEIIDYNT.FSGV.EDDL.NIRTSIRDVQA.
Retrocopy GMFAVNCEMSYTVKGLELT*VTVVDSSFQMVCDTFVKPDEEIIDYNTKFSGVEEDDLRNIRTSIRDVQAV

Parental  LLNLFSADTILIGHSFEQCLYALKLIHTCVVDTTVMFPHRLGLPHKRSLGSLVADYLQRIIQDDVFEGHN
          LLNLFSADTILIGHSFE..LYALKLIHTCVVDT.VMFPHR.GLPHKRSL.SLVADYLQRIIQDD...GHN
Retrocopy LLNLFSADTILIGHSFE*SLYALKLIHTCVVDTAVMFPHRRGLPHKRSLESLVADYLQRIIQDD---GHN

Parental  TSEKAKACMELVLWKVKEDLKGKK
          TSEK.KACMELVLW.VKEDLKGKK
Retrocopy TSEKEKACMELVLWRVKEDLKGKK

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	0.50 RPM
SRP017611_kidney	0.00 RPM	0.51 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1327 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1327 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1327 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021090	3 retrocopies	retro_ocun_123, retro_ocun_1327 , retro_ocun_201,