RetrogeneDB ID: retro_ocun_32

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02082089:14057..14789(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021978
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006103
• Aliases: None
• Description: None

Sequence

>retro_ocun_32
ATGCCTGGTAAAACAAATGTTTCCAAGAAGTCTCAGCAGGTAAAAAGAAATCCAAAAAGAAAAATTGATGATGAAGAAGT
AAAGTTGCCAGAGAAAGAGGTTAGAAAAACAGTAAAAAGAAATAAAAATCATACAAAACGTCTGTCTTCTGAAGGGCAAA
CAAATCTAAAAAGGGTAAAGATAAGCTCCACCAAGAGAAAAACTTGGCAGCCTCTTTCAAGGAGTACCAGAGAGCATTTG
CAAACTATGATGGAATCAGTAATAATAGCAATTTTGAGTAACACTATTAAAGACAAAGAACAAATTCAATATCATCTCAA
CTGTCTGAAGAAAAGGTTGCTACAACTGTATGAAACTCTCAAAGCCCCTTCCAAAAAGCTAAAAGATTTAACTAATGTGT
CAAGTCTACTGAATATGGAAAGAGCACAGGAAAGAGTTAATGAAGATGGTCTGACATTACTACAGGAAGAAATAGATAAA
CTAGTGGAGACCACAGAGTTGATGACTGGGAAGATTCAGAGCCTAAAGAACAAAATACAGATTCTGGCAAGTGAGGTAGA
AGAGGAGGAGCAGAAGATGCTTCAAATGAGTAGTAGCGGGGTACTCTCTCTTCCACAGCTTTCTCAGAACAGTCTGAAAG
CACCCACACTTCAGAAAGAAATTTTGACACTAATTCCAAACCAGGATGCTCTCCTAAAGGACTTGGATGTTCTTCATACT
TCATCCGAGATT

Alignment

ORF - retro_ocun_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.0 %
• Parental protein coverage: 92.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGKTNVSKKSQQLKRNPKRKIDDEEVKLPEKEVRKTVKRNKNHTKRLSSEAMTGQTNLKRVKISSTKRK
          MPGKTNVSKKSQQ.KRNPKRKIDDEEVKLPEKEVRKTVKRNKNHTKRLSSE...GQTNLKRVKISSTKRK
Retrocopy MPGKTNVSKKSQQVKRNPKRKIDDEEVKLPEKEVRKTVKRNKNHTKRLSSE---GQTNLKRVKISSTKRK

Parental  TWQPLSRSTREHLQTMMESVIITILSNSIKDKEQIQYHLNCLKKRLLQLYETLKAPSKKLKDLTNVSSLL
          TWQPLSRSTREHLQTMMESVII.ILSN.IKDKEQIQYHLNCLKKRLLQLYETLKAPSKKLKDLTNVSSLL
Retrocopy TWQPLSRSTREHLQTMMESVIIAILSNTIKDKEQIQYHLNCLKKRLLQLYETLKAPSKKLKDLTNVSSLL

Parental  NMERAQERVNEDGLTLLQEEIDKLVETTELMTGKIQSLKNKIRILASEVEEEEQKVKHFLLLDSSGVLSL
          NMERAQERVNEDGLTLLQEEIDKLVETTELMTGKIQSLKNKI.ILASEVEEEEQK....L...SSGVLSL
Retrocopy NMERAQERVNEDGLTLLQEEIDKLVETTELMTGKIQSLKNKIQILASEVEEEEQKM---LQMSSSGVLSL

Parental  PQLSQNSLKAPTLQKEILTLIPNQDALLKDLDVLHTSSEV
          PQLSQNSLKAPTLQKEILTLIPNQDALLKDLDVLHTSSE.
Retrocopy PQLSQNSLKAPTLQKEILTLIPNQDALLKDLDVLHTSSEI

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	0.28 RPM	0.77 RPM
SRP017611_kidney	1.22 RPM	0.61 RPM
SRP017611_liver	3.16 RPM	5.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_32 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_32 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_32 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000345	1 retrocopy	retro_chof_1088,
Oryctolagus cuniculus	ENSOCUG00000006103	1 retrocopy	retro_ocun_32 ,
Ictidomys tridecemlineatus	ENSSTOG00000001426	1 retrocopy	retro_itri_1111,
Tupaia belangeri	ENSTBEG00000004322	1 retrocopy	retro_tbel_1115,