RetrogeneDB ID: retro_ocun_474

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:47687252..47687810(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000012098
• Aliases: None
• Description: None

Sequence

>retro_ocun_474
ATGGCGTCGCCCGTGCTGGTTGTGATGTTTCAGCAGCACCAGGCATTCCGGGTACTGTTCCGAAACTGGTGGGAGCAACT
ACAGCGGAAGCTTCAACTGGGCCACCCAGGCTTTCCTCGTGTGCCATGGGAACCAGCATTAGCAGTCCAGGGACCAACCA
TCTTTACAGAGCCAAAGGATACCAGTGAGAGTGAGAATTCCAGCCTTTTGGACAGTATCTTTTGGATGGCAGCTCCTAAA
AACAGACGCACCATTGAAGTTAATCGGTGTAGGAGAAGAAATCCTCATAAGCTTATTAAAGTTAAGAATAATATAGACGT
GTGTCCAGAATGTGGCCACCTGAAACAGAAGCACGTCCTTTGTGGCTATTGCTATGAGAAAGTGCGTAAGGAGACTGCAG
CAATCAGACAACAGATAGGAAAACAAGAAGGAGGCCCTTTTAAGGCTCCTACGGTAGAGACTGTGGTGCTGTACACGGGG
GAGACACCATCTGAAGAAGATCAGGGCAAGAGGATCATCGAACGGGACAGGAAGCGGCCATCCTGGTTCACCCAGAAT

Alignment

ORF - retro_ocun_474 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPVLVVMFQQHQAFRVLFRNWWEQLQRKLQLGHPGFPRVPWEPALAVQGPTIFTEPKDTSESENSSLL
          MASPVLVVMFQQHQAFRVLFRNWWEQLQRKLQLGHPGFPRVPWEPALAVQGPTIFTEPKDTSESENSSLL
Retrocopy MASPVLVVMFQQHQAFRVLFRNWWEQLQRKLQLGHPGFPRVPWEPALAVQGPTIFTEPKDTSESENSSLL

Parental  DSIFWMAAPKNRRTIEVNRCRRRNPHKLIKVKNNIDVCPECGHLKQKHVLCGYCYEKVRKETAAIRQQIG
          DSIFWMAAPKNRRTIEVNRCRRRNPHKLIKVKNNIDVCPECGHLKQKHVLCGYCYEKVRKETAAIRQQIG
Retrocopy DSIFWMAAPKNRRTIEVNRCRRRNPHKLIKVKNNIDVCPECGHLKQKHVLCGYCYEKVRKETAAIRQQIG

Parental  KQEGGPFKAPTVETVVLYTGETPSEEDQGKRIIERDRKRPSWFTQN
          KQEGGPFKAPTVETVVLYTGETPSEEDQGKRIIERDRKRPSWFTQN
Retrocopy KQEGGPFKAPTVETVVLYTGETPSEEDQGKRIIERDRKRPSWFTQN

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	1.16 RPM	1.88 RPM
SRP017611_kidney	0.71 RPM	1.93 RPM
SRP017611_liver	0.31 RPM	0.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_474 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_474 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
Mustela putorius furo	ENSMPUG00000018146	1 retrocopy	retro_mputfur_60,
Mus musculus	ENSMUSG00000015672	1 retrocopy	retro_mmus_61,
Oryctolagus cuniculus	ENSOCUG00000012098	1 retrocopy	retro_ocun_474 ,
Otolemur garnettii	ENSOGAG00000016806	2 retrocopies	retro_ogar_1965, retro_ogar_2797,
Rattus norvegicus	ENSRNOG00000015989	1 retrocopy	retro_rnor_460,
Ictidomys tridecemlineatus	ENSSTOG00000013340	1 retrocopy	retro_itri_1122,
Tarsius syrichta	ENSTSYG00000014296	1 retrocopy	retro_tsyr_1710,