RetrogeneDB ID: retro_ocun_133

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02080821:13654..15184(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023353
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDZK1
• Ensembl ID: ENSOCUG00000024935
• Aliases: None
• Description: PDZ domain containing 1 (PDZK1), mRNA [Source:RefSeq mRNA;Acc:NM_001082151]

Sequence

>retro_ocun_133
GAATGCAAACTGTCCAAAGAAGAAGGGCAAAACTATGGCTTCTTCCTGCAAATCGAGAAAGACACGGAGGGCCACCTGGT
CCGGGTGATTGAGAAGGGCAGCCCTGCGGAGAAGGCCGGCCTGCAGGATGGAGACCACGTTCTCAGGATCAACGGGGTCT
TCGTGGACAAGGAAGAGCATATGCAGGTGGTGGATCTGGTGAGAAAGAGTGGGAATGCAGTGACTCTACTAGTTCTGGAT
GGGAATTCCTATGAGAAAGCTGTGAAAAAACAGGTAGATTTGAAAGAGTTGGGTCAGAGTCGGCAGGAGGCGGATTTGCG
TGATGAGAACGTGGCCCCTGTGATGAATGGAGAAGTGGAGACCTGGACGCAGCCGCGACTCTGCTACCTGGTGAAGCAGG
GGAACAGCTACGGCTTCTCCCTGAAAACCGTGCAAGGTAAAAAGGGCGTGTACATGACTGATATCATCCCTCAAAACGTG
GCTATGAAGGCTGGCGTCCTGGCTGATGACCACTTGATTGAAGTGAACGGAGAGAATGTAGAAGATGCCAGTCACGAGGA
GGTGGTTGAAAAGGTGAAGTCGGGAAACCGTATCATGTTCCTTCTGGTGGACAAAGAAACTGAGAAACGGCACAGCGAGC
AGAAGATAGAGTTCAGGAGAGAAGCGGCCAGTTTGAAGCTGCTGCCCCACCAGCCCCGCATTGTGGAGATGAAGAAGGGA
AGCAGTGGCTATGGTTTCTATCTGAAGGCAGGCCCGGAACAGAGAGGCCAAATCATCAAGGACATAGATTCTGGAAGTCC
AGCAGAGGCGGCTGGCTTGAAGAACAATGACCTGGTAATTGCTGTCAACGGCAAGTCTGTGGAAGCCCTTGATCATGACG
GTGTGGTGGAGCTGATTAAAAAGGGTGGAGATCAGACTTCACTGTTGGTGGTGGACAAAGAGGCGGACAGCATGTATAGA
CTGGCTCATTTTTCTCCATTTCTCTACTATCAAAGTCAAGAACTGCCTAATGGTTCTGTGAAGGAGGTTGCAGATCCTAC
CCCTGTTCCTCCGGAAGTCTCAAGTCCAGATCCTACAGAGGAAGTAGAAGATCATAAGCCTAAACTCTGCAGGCTGGATA
AAGGGGAAAATGGCTATGGCTTTCACTTAAATGCGATCCGGGGCCTGCCAGGCTCATTTGTCAAAGAGGTACAGAAGGGC
AGCCCTGCTGACTCGGCTGGGTTGGAGGATGAGGATATCATCATTGAAGTGAATGGGGTGAACGTGCTGGATGAACCCTA
TGAGAAGGTGGTGGACAGAATCCAAAGCAGTGGGGACAATGTCACACTATTAGTCTGTGGAAAGAAGGCCTACGAATATT
TCCAAGCTAAGAAAATCCCTATTGTTTCCTCCATGGCTCTTCCATTGGCTATACCTCCGGATTCTCAAGGAGTGTTGGTG
GAATTGGAGTACAACTTGCACGAGGCAAAAGAACGAGCACACAGTACAGCTTCAAATTCTTCTTCCAATTCTGAAGATAC
CGAGCTGTAA

Alignment

ORF - retro_ocun_133 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ECKLSKEEGQNYGFFLRIEKDTEGHLVRVIEKGSPAEKAGLQDGDRVLRINGVFVDKEEHMQVVDLVRKS
          ECKLSKEEGQNYGFFL.IEKDTEGHLVRVIEKGSPAEKAGLQDGD.VLRINGVFVDKEEHMQVVDLVRKS
Retrocopy ECKLSKEEGQNYGFFLQIEKDTEGHLVRVIEKGSPAEKAGLQDGDHVLRINGVFVDKEEHMQVVDLVRKS

Parental  GNAVTLLVLDGNSYEKAVKKQVDLKELGQSRQEADLRDENVAPVMNGGVETWTQPRLCYLVKQGNSYGFS
          GNAVTLLVLDGNSYEKAVKKQVDLKELGQSRQEADLRDENVAPVMNG.VETWTQPRLCYLVKQGNSYGFS
Retrocopy GNAVTLLVLDGNSYEKAVKKQVDLKELGQSRQEADLRDENVAPVMNGEVETWTQPRLCYLVKQGNSYGFS

Parental  LKTVQGKKGVYMTDIIPQSVAMKAGVLADDHLIEVNGENVEDASHEEVVEKVKKSGNRIVFLLVDKETEK
          LKTVQGKKGVYMTDIIPQ.VAMKAGVLADDHLIEVNGENVEDASHEEVVEKVK.SGNRI.FLLVDKETEK
Retrocopy LKTVQGKKGVYMTDIIPQNVAMKAGVLADDHLIEVNGENVEDASHEEVVEKVK-SGNRIMFLLVDKETEK

Parental  RHSEQKIEFRREAASLKLLPHQPRIVEMRKGSSGYGFYLKAGPEQRGGRVGQIIKDIDSGSPAEAAGLKN
          RHSEQKIEFRREAASLKLLPHQPRIVEM.KGSSGYGFYLKAGPEQR....GQIIKDIDSGSPAEAAGLKN
Retrocopy RHSEQKIEFRREAASLKLLPHQPRIVEMKKGSSGYGFYLKAGPEQR----GQIIKDIDSGSPAEAAGLKN

Parental  NDLVIAVNGKSVEALDHDGVVELIKKGGDQTSLLVVDKEADSMYRLAHFSPFLYYQSQELPNGSVTEVAA
          NDLVIAVNGKSVEALDHDGVVELIKKGGDQTSLLVVDKEADSMYRLAHFSPFLYYQSQELPNGSV.EVA.
Retrocopy NDLVIAVNGKSVEALDHDGVVELIKKGGDQTSLLVVDKEADSMYRLAHFSPFLYYQSQELPNGSVKEVAD

Parental  PTPVPPEVSSPDPTEEVEDHKPKLCRLDKGENGYGFHLNAIRGLPGSFVKEVQKGSPADLAGLEDEDIII
          PTPVPPEVSSPDPTEEVEDHKPKLCRLDKGENGYGFHLNAIRGLPGSFVKEVQKGSPAD.AGLEDEDIII
Retrocopy PTPVPPEVSSPDPTEEVEDHKPKLCRLDKGENGYGFHLNAIRGLPGSFVKEVQKGSPADSAGLEDEDIII

Parental  EVNGVNVLDEPYEKVVDRIQSSGDNVTLLVCGKKAYEYFQAKKIPIVSSMALPLAIPPDSQGVLAELEYN
          EVNGVNVLDEPYEKVVDRIQSSGDNVTLLVCGKKAYEYFQAKKIPIVSSMALPLAIPPDSQGVL.ELEYN
Retrocopy EVNGVNVLDEPYEKVVDRIQSSGDNVTLLVCGKKAYEYFQAKKIPIVSSMALPLAIPPDSQGVLVELEYN

Parental  LHEAKERAHSTASNSSSNSEDTEL
          LHEAKERAHSTASNSSSNSEDTEL
Retrocopy LHEAKERAHSTASNSSSNSEDTEL

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	0.39 RPM	22.30 RPM
SRP017611_kidney	27.67 RPM	532.22 RPM
SRP017611_liver	3.47 RPM	99.35 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_133 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011153	1 retrocopy	retro_cfam_298,
Dasypus novemcinctus	ENSDNOG00000000375	2 retrocopies	retro_dnov_1158, retro_dnov_1857,
Myotis lucifugus	ENSMLUG00000028785	1 retrocopy	retro_mluc_1116,
Oryctolagus cuniculus	ENSOCUG00000024935	1 retrocopy	retro_ocun_133 ,