RetrogeneDB ID: retro_ocun_23

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:6792633..6793452(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027568
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000001096
• Aliases: None
• Description: None

Sequence

>retro_ocun_23
ATGGACAAGTCAGAAATGGACCCTCTTGACCACATGACATCTGATGCAACTATGGAAATTGATAATGAAAGTGATGACAG
TTCATCTGGTAGCAGTGTGTTTAAAATTCAATGTGTTCCTTCCTCACCTAATTGGAGGCCAAAAAACACCATTAGAAAAC
CTATTCATTCATCTAAAATTGTCGAAACAACAGATTCTTCAAGTGATTCATCTGTAGAACCAAGACCATTGACACTAAAA
GCACTTATTGCAAAATTTAAGAAAAAGAAACGTAAAAGGAGAAAACAGAAATACAAGGCAACAGGAAGGCCAGTAGGCAG
GCCTAAAGGACGGAAAAACACTAAAATATCACATGTAGATAAAAACCAATTTAAAGACAAAGGACCTAGGTTCTCATTTT
TAGAATCAGAGAATGGAACTCAACCATCACCTTGGAGGAAAATTTTAACCTTTGAGCAAGCAGTTGCAAGAGGATTTTTT
AATTACATTGAAAAACTGAAGTATGAATATCACCTGAAAGAATCTCTGAAACAAATGGATGTTGGTGATGATTTAGAAAA
GGAAGATCTTGACAGTCGAAGATACAAGTATTTGGATGATGATGGATCTATATCTCCTATTGAAGAATCAGTAGCGGAGG
ATGAGGAAGCAGCACACCCTGAACAGGAGGAATGTGATATCAAATTGGTTGACAGTAGTTGTTTCATAATAAATTCGGAA
TTCCCAAAACTGATGAATGTGAATTCAGAACAGAATGTGAAAGAAGCCGTTTCCTATAAAAAGAGAGCCTCAAAAGTCAA
AAACACTGCACAGAAGATG

Alignment

ORF - retro_ocun_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDKSEMDPLDHMTSDATMEIDNESDDSSSGSSVFKTQCVPSSPNWRPKNTIRKPIHSSKIVETTDSSSDS
          MDKSEMDPLDHMTSDATMEIDNESDDSSSGSSVFK.QCVPSSPNWRPKNTIRKPIHSSKIVETTDSSSDS
Retrocopy MDKSEMDPLDHMTSDATMEIDNESDDSSSGSSVFKIQCVPSSPNWRPKNTIRKPIHSSKIVETTDSSSDS

Parental  SVEPRPLTLKALIAKFKKKKRKRRKQKYKATGRPVGRPKGRKNTKISHVDKNQFKDKGPRFSFLESENGT
          SVEPRPLTLKALIAKFKKKKRKRRKQKYKATGRPVGRPKGRKNTKISHVDKNQFKDKGPRFSFLESENGT
Retrocopy SVEPRPLTLKALIAKFKKKKRKRRKQKYKATGRPVGRPKGRKNTKISHVDKNQFKDKGPRFSFLESENGT

Parental  QPSPWRKILTFEQAVARGFFNYIEKLKYEYHLKESLKQMDVGDDLEKEDLDSRRYKYLDDDGSISPIEES
          QPSPWRKILTFEQAVARGFFNYIEKLKYEYHLKESLKQMDVGDDLEKEDLDSRRYKYLDDDGSISPIEES
Retrocopy QPSPWRKILTFEQAVARGFFNYIEKLKYEYHLKESLKQMDVGDDLEKEDLDSRRYKYLDDDGSISPIEES

Parental  VAEDEEAAHPEQEECDIKLVDSSCFIINSEFPKL-NVNSEQNVKEAVSSKKRASKVKNTAQKM
          VAEDEEAAHPEQEECDIKLVDSSCFIINSEFPKL.NVNSEQNVKEAVS.KKRASKVKNTAQKM
Retrocopy VAEDEEAAHPEQEECDIKLVDSSCFIINSEFPKLMNVNSEQNVKEAVSYKKRASKVKNTAQKM

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	14.07 RPM
SRP017611_kidney	0.00 RPM	9.22 RPM
SRP017611_liver	0.00 RPM	6.17 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_23 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_23 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_23 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013436	1 retrocopy	retro_chof_405,
Myotis lucifugus	ENSMLUG00000011431	1 retrocopy	retro_mluc_2033,
Monodelphis domestica	ENSMODG00000008546	1 retrocopy	retro_mdom_1216,
Oryctolagus cuniculus	ENSOCUG00000001096	2 retrocopies	retro_ocun_101, retro_ocun_23 ,
Otolemur garnettii	ENSOGAG00000002521	1 retrocopy	retro_ogar_1139,
Sarcophilus harrisii	ENSSHAG00000005874	1 retrocopy	retro_shar_566,
Tarsius syrichta	ENSTSYG00000014258	1 retrocopy	retro_tsyr_1107,