RetrogeneDB ID: retro_ocun_97

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:80759292..80760306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000029302
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000012520
• Aliases: None
• Description: None

Sequence

>retro_ocun_97
ATGGCGGATGCAGTACCCCAACCCGTCAAGAGAAAGCGCGAATGGGATGCTGAGGAGGCGGAAGCCCCCAGTCCAGAGAA
AAAGGACGGCGGCGTTGGAAATGGGACCCCTGCTCCTGTCAGCTTGCCGTTCTCCGGCTTTAGACTACAAAAAGTGCTGA
GGGAGTCTGCGCGGGACAAAATCATTTTCTTACATGGGAAGGTGAATGAGGCTTCTGGGGATGGGGACGGAGAGGATGCT
GTTGTGATCATGGAAAAGACGCCATTTCAGGTGGACCAGGTGGCCCAGCTCCTGACCGGCAGCCCTGAACTCCAGTTGCA
GTTCTCCAATGATATCTACAGCACCTATCACCTGTTCCCTCCAAGGCAACTGAGTGACATAAAGACGACCGTGGTCTACC
CTGCCACAGAGAAACACCTGCAGAAGTACCTGCGCCAGGACTTGCACCTGGTCCGGGAGACAGGCGATGACTACAAGAAT
GTTACCTTACCCTACCTGGAGTCCCAGAGCCTCAGCATCCAGTGGGTATACAACATTCTCGACAAGAAAGCTGAAGTCGA
CCGGATTGTTTTTGAGAACCCAGATCCCTCAGATGGCTTTGTCCTCATCCCCGACCTCAAGTGGAACCAACAGCAGCTTG
ATGACCTGTACTTGATCGCCATCTGCCATCGCCGGGGCATCAAATCGCTTCGGGACCTGACGCCAGAGCATCTGCCACTG
CTCAGGAATATCCTCCATGAAGGCCAGGCAGCCATCCTGCAGCGCTACCAGGTGAAGGGGGACCGCCTGCGTGTGTACCT
GCACTACCTACCCTCCTACTACCACCTGCACGTGCACTTCACTGCCCTGGGCTTCGAAGCCCCCGGCTCGGGCGTGGAGC
GAGCTCACCTGCTGGCTGAGGTGATCGAGAACCTGGAGTGCAACCCCAAGCACTATCAGCAGCGCTCACTGACCTTCACC
CTCAGGGCCGACGACCCCCTCCTCAAGCTCCTGCAGGAGGCCCAGCAGCGCTGA

Alignment

ORF - retro_ocun_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAVPQPVKRKREWDAEEAEAPSPEKKDGGVGNGTPAPVSLPFSGFRLQKVLRESARDKIIFLHGKVNE
          MADAVPQPVKRKREWDAEEAEAPSPEKKDGGVGNGTPAPVSLPFSGFRLQKVLRESARDKIIFLHGKVNE
Retrocopy MADAVPQPVKRKREWDAEEAEAPSPEKKDGGVGNGTPAPVSLPFSGFRLQKVLRESARDKIIFLHGKVNE

Parental  ASGDGDGEDAVVIMEKTPFQVDQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLSDIKTTVVYPATEKHL
          ASGDGDGEDAVVIMEKTPFQVDQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLSDIKTTVVYPATEKHL
Retrocopy ASGDGDGEDAVVIMEKTPFQVDQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLSDIKTTVVYPATEKHL

Parental  QKYLRQDLHLVRETGDDYKNVTLPYLESQSLSIQWVYNILDKKAEVDRIVFENPDPSDGFVLIPDLKWNQ
          QKYLRQDLHLVRETGDDYKNVTLPYLESQSLSIQWVYNILDKKAEVDRIVFENPDPSDGFVLIPDLKWNQ
Retrocopy QKYLRQDLHLVRETGDDYKNVTLPYLESQSLSIQWVYNILDKKAEVDRIVFENPDPSDGFVLIPDLKWNQ

Parental  QQLDDLYLIAICHRRGIKSLRDLTPEHLPLLRNILHEGQAAILQRYQVKGDRLRVYLHYLPSYYHLHVHF
          QQLDDLYLIAICHRRGIKSLRDLTPEHLPLLRNILHEGQAAILQRYQVKGDRLRVYLHYLPSYYHLHVHF
Retrocopy QQLDDLYLIAICHRRGIKSLRDLTPEHLPLLRNILHEGQAAILQRYQVKGDRLRVYLHYLPSYYHLHVHF

Parental  TALGFEAPGSGVERAHLLAEVIENLECNPKHYQQRSLTFTLRADDPLLKLLQEAQQ
          TALGFEAPGSGVERAHLLAEVIENLECNPKHYQQRSLTFTLRADDPLLKLLQEAQQ
Retrocopy TALGFEAPGSGVERAHLLAEVIENLECNPKHYQQRSLTFTLRADDPLLKLLQEAQQ

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	4.08 RPM	1.49 RPM
SRP017611_kidney	1.11 RPM	1.62 RPM
SRP017611_liver	2.70 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_97 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_97 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_97 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008896	1 retrocopy	retro_cjac_1833,
Oryctolagus cuniculus	ENSOCUG00000012520	1 retrocopy	retro_ocun_97 ,