RetrogeneDB ID: retro_ocun_1718

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018806:197947..198809(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001258
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNASE2
• Ensembl ID: ENSOCUG00000021573
• Aliases: None
• Description: deoxyribonuclease II, lysosomal [Source:HGNC Symbol;Acc:2960]

Sequence

>retro_ocun_1718
GGCGCGGGCTCCATCAACAGCTCGGCGGGGGCCGTGGGCCGCAGCCTGCTGCCGCTGTACCGGAGCAACGCTAGCCAGCT
CGCGTTCCTGCTCTACAATGACCAACCGCCCAAAGCCAGTAGAGCCCAGGGCTCCTCCAGCCACGGCCACACAAAGGGTG
TCCTGCTCCTGGACCAAGAAGGAGGCCTCTGGCTGGTGCACAGCGTGCCCCGTTTCCCACCCCCACCCTCTGCTGGCGTG
TACAGCTGGCCCCACAATGCCCAAACCTATGGGCAGATGCTGCTCTGCGTGTCTTTTCCCCTCAGCCAGTTTCAGAGCAT
TGGCAGGCAGCTGGCCTACACCTACCCTCTGGTCTATGACCACCAGCTGGATGGGGTCTTTGTCCAGAAATTCCCCGACC
TGGAGGAAGTGATCAAGGGCCACCACGTGAGCCACGAACCGTGGAACAGCAGCCTTACGCTCACGTCACAGGCAGGGGCC
ACCTTCCAGTTTTGCCAAAGCCGGCGGGTTCGGGGATGACCTGTACTCCGGCTGGCTGGCGGCAGCCCTTCGTAGCAACC
TGCAGGTCCAGTTCTGGCAAAATTCTCCCGGCGTCCTGCCCTCCAACTGCTCAGGGACCCAGCAGGTTCTGGACGTAACC
CAGACAGCTTTCCCTGGGCCGACCGGCCCCACGTTCAGCGCTGCAGAGGACCACTCCAAATGGTGCGTGGCCCCAGAGGG
ACCGTGGGCCTCCGTGGGCCACATGAATCGGAACCGCGGCGAAGAGCACCGGGGTGGGGGCATGCTGTGCTCCCGGCTGC
CCGCGCTCTGGAAGGCTTTCCAGCCCCTGGTGAAAGCCTGGCAGCCCTGCAGCGAGGAGGAG

Alignment

ORF - retro_ocun_1718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.81 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GAGSINSSAGAVGRSLLPLYRSNASQLAFLLYNDQPPKAGRAQ-SSSHGHTKGVLLLDQEGGLWLVHSVP
          GAGSINSSAGAVGRSLLPLYRSNASQLAFLLYNDQPPKA.RAQ.SSSHGHTKGVLLLDQEGGLWLVHSVP
Retrocopy GAGSINSSAGAVGRSLLPLYRSNASQLAFLLYNDQPPKASRAQGSSSHGHTKGVLLLDQEGGLWLVHSVP

Parental  RFPPPPSAGAYSWPHNAQTYGQMLLCVSFPLGQFQSIGRQLTYTYPLVYDHQLDGVFAQKFPDLEEVIKG
          RFPPPPSAG.YSWPHNAQTYGQMLLCVSFPL.QFQSIGRQL.YTYPLVYDHQLDGVF.QKFPDLEEVIKG
Retrocopy RFPPPPSAGVYSWPHNAQTYGQMLLCVSFPLSQFQSIGRQLAYTYPLVYDHQLDGVFVQKFPDLEEVIKG

Parental  HHVSHEPWNSSVTLTSQAGATFQSFAKA-GGFGDDLYSGWLAAALRSNLQVQFWQNSPGVLPSNCSGTQQ
          HHVSHEPWNSS.TLTSQAGATFQ.F....GGFGDDLYSGWLAAALRSNLQVQFWQNSPGVLPSNCSGTQQ
Retrocopy HHVSHEPWNSSLTLTSQAGATFQ-FCQS>GGFGDDLYSGWLAAALRSNLQVQFWQNSPGVLPSNCSGTQQ

Parental  VLDVTQTAFPGPTGPTFSATEDHSKWCVAPEGPWACVGDMNRNRGEEHRGGGMLCSRLPALWKAFQPLVK
          VLDVTQTAFPGPTGPTFSA.EDHSKWCVAPEGPWA.VG.MNRNRGEEHRGGGMLCSRLPALWKAFQPLVK
Retrocopy VLDVTQTAFPGPTGPTFSAAEDHSKWCVAPEGPWASVGHMNRNRGEEHRGGGMLCSRLPALWKAFQPLVK

Parental  AWQPCSEEE
          AWQPCSEEE
Retrocopy AWQPCSEEE

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	0.06 RPM	2.76 RPM
SRP017611_kidney	0.61 RPM	10.44 RPM
SRP017611_liver	0.08 RPM	7.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1718 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1718 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000021573	1 retrocopy	retro_ocun_1718 ,