RetrogeneDB ID: retro_ocun_14

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:30686538..30687354(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000009991
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005025
• Aliases: None
• Description: None

Sequence

>retro_ocun_14
ATGGCGGCGGATGGAGAGCGTTCCCCGCTGCTGTGCGAACCCATCGACGGAGGCGCTGGCGGCAACGGTTTAGTGGGGCC
GGGAGGGAGTGGGGCTGGGCCCGGGGGAGGCCTGACCCCCTCCGCATTCCCCCCGTTCCCCGAGGGGCACCCAGCTGTGT
TGCCTGGGGAGGACCCACCCCCCTACTCACCGCTGACCAGCCCGGATAGTGGGAGCGCCCCCATGATCACCTGCCGAGTC
TGCCATTCTCTCATCAATGTGGAAGGCAAGATGCATCAGCATGTAGTCAAATGTGGTGTCTGCAACGAAGCCACTCCCAT
CAAGAATGCACCTCCAGGAAAAAAATATGTCCGATGTCCCTGTAACTGCCTCCTTATCTGCAAAGTGACTTCCCAGCGGA
TTGCCTGTCCTCGGCCCTACTGCAAAAGAATCATCAACCTCGGACCCGTGCACCCAGGACCTCTGAGTCCAGAACCACAG
CCCGTGGGTGTCAGAGTCACCTGTGGACATTGCAAGAATACTTTCCTGTGGACAGAGTTCACAGACCGAACCTTGGCGCG
TTGCCCTCACTGCAGGAAAGTGTCATCTATTGGGCGCAGATACCCACGAAAGAGATGTGTCTGTTGCTTCTTGCTTGGTT
TACTCTTTGCGGTCACTGCTACTGGCCTTGCTTTTGGCACACGGAAGCATGCACGGCAGTATGGAGGCATCTACGCAGCC
TGGGCGTTTGTGATCCTGTTGGCTGTGCTGTGTTTGGGCAGGGCCCTCTATTGGGCCTGCATGAAGGTCAGCCACCCTGT
CCAGAACTTCTCCTGA

Alignment

ORF - retro_ocun_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.8 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVGPGGSGAGPGGGLTPSAPPYGAGKHAPPQAFPPFPEGHPAVLPGEDPPPYSPLTSPDSGSAPMITCRV
          L..P...GAG..G...P.....G.G....P.AFPPFPEGHPAVLPGEDPPPYSPLTSPDSGSAPMITCRV
Retrocopy LCEPIDGGAGGNGLVGPGGSGAGPGGGLTPSAFPPFPEGHPAVLPGEDPPPYSPLTSPDSGSAPMITCRV

Parental  CHSLINVEGKMHQHVVKCGVCNEATPIKNAPPGKKYVRCPCNCLLICKVTSQRIACPRPYCKRIINLGPV
          CHSLINVEGKMHQHVVKCGVCNEATPIKNAPPGKKYVRCPCNCLLICKVTSQRIACPRPYCKRIINLGPV
Retrocopy CHSLINVEGKMHQHVVKCGVCNEATPIKNAPPGKKYVRCPCNCLLICKVTSQRIACPRPYCKRIINLGPV

Parental  HPGPLSPEPQPVGVRVTCGHCKNTFLWTEFTDRTLARCPHCRKVSSIGRRYPRKRCVCCFLLGLLLAVTA
          HPGPLSPEPQPVGVRVTCGHCKNTFLWTEFTDRTLARCPHCRKVSSIGRRYPRKRCVCCFLLGLL.AVTA
Retrocopy HPGPLSPEPQPVGVRVTCGHCKNTFLWTEFTDRTLARCPHCRKVSSIGRRYPRKRCVCCFLLGLLFAVTA

Parental  TGLAFGTWKHARRYGGIYAAWAFVILLAVLCLGRALYWACMKVSHPVQNFS
          TGLAFGT.KHAR.YGGIYAAWAFVILLAVLCLGRALYWACMKVSHPVQNFS
Retrocopy TGLAFGTRKHARQYGGIYAAWAFVILLAVLCLGRALYWACMKVSHPVQNFS

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	2.04 RPM	35.60 RPM
SRP017611_kidney	1.22 RPM	22.20 RPM
SRP017611_liver	0.62 RPM	17.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_14 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_14 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000000723	2 retrocopies	retro_ocun_1391, retro_ocun_1704,
Oryctolagus cuniculus	ENSOCUG00000005025	1 retrocopy	retro_ocun_14 ,