RetrogeneDB ID: retro_ocun_1023

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:38602194..38602569(-)
• Located in intron of: ENSOCUG00000009159

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010114
• Aliases: None
• Description: None

Sequence

>retro_ocun_1023
ATGCTGTCCCGTCTGCTGAAGGAACACCAGGCCAAGCAGAATGAACGCAAGGAGCTGCAGGAGAAGAGGAGGCGAGAGGC
AATCACGGCCGCGACCTGCCTGACCGAAGCCCTGGTGGACCACCTCAACGTGGGTGTGGCCCAGGCCTACGTGAACCAGA
GGAAGCTGGACCACAAGGTGAAGACCCTGCAGGCCCAGGCTGCCCAGTTTGCCAAGCAGACAGGCCAGTGGATTGGGATG
GTGGAGAACTTCAACCAGGCTCTCAAGGAAATCGGGGATGTGGAGAACTGGGCTCGGAGCATTGAGCTGGACATGCACAC
CATTGCCACCGCGCTGGAATACGTGTACAAGGGACAGCTGCAGTCGGCCCCCTCC

Alignment

ORF - retro_ocun_1023 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYVNQRKLDREVKTLQAQAAQF
          MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYVNQRKLD..VKTLQAQAAQF
Retrocopy MLSRLLKEHQAKQNERKELQEKRRREAITAATCLTEALVDHLNVGVAQAYVNQRKLDHKVKTLQAQAAQF

Parental  AKQTGQWIGMVENFNQALKEIGDVENWARSIELDMRTIATALEYVYKGQLQSAPS
          AKQTGQWIGMVENFNQALKEIGDVENWARSIELDM.TIATALEYVYKGQLQSAPS
Retrocopy AKQTGQWIGMVENFNQALKEIGDVENWARSIELDMHTIATALEYVYKGQLQSAPS

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	0.11 RPM	18.27 RPM
SRP017611_kidney	0.10 RPM	73.99 RPM
SRP017611_liver	0.08 RPM	6.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1023 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011918	1 retrocopy	retro_btau_878,
Callithrix jacchus	ENSCJAG00000008026	1 retrocopy	retro_cjac_148,
Cavia porcellus	ENSCPOG00000001818	2 retrocopies	retro_cpor_1260, retro_cpor_846,
Macropus eugenii	ENSMEUG00000001570	3 retrocopies	retro_meug_12, retro_meug_1307, retro_meug_242,
Oryctolagus cuniculus	ENSOCUG00000010114	1 retrocopy	retro_ocun_1023 ,
Pteropus vampyrus	ENSPVAG00000017748	1 retrocopy	retro_pvam_121,
Sus scrofa	ENSSSCG00000000359	1 retrocopy	retro_sscr_850,
Ictidomys tridecemlineatus	ENSSTOG00000010338	1 retrocopy	retro_itri_467,