RetrogeneDB ID: retro_ocun_382

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:99432144..99432837(-)
• Located in intron of: ENSOCUG00000011238

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL3
• Ensembl ID: ENSOCUG00000006789
• Aliases: None
• Description: ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) [Source:HGNC Symbol;Acc:12515]

Sequence

>retro_ocun_382
ATGGAGGGTCAGCGCTGACTGCCGCTGGAGGCTAATCCAGAGGTCACCAACCAGTTTCTCAAGCAATTAGGTCTGCATCC
TAACTGGCAGTTTGTTGATGTATATGGAATGGATCCTGAACTTCTTAGCATGGTACCAAGACCAGTTTGTGCAGTGTTAC
TTCTCTTCCCTATTACAGAAAAGTATGAAATATTCAGAACAGAAGAAGAGGAAAAAATAAAATCTCAGGGACAGGATGTG
ACATCATCAGTATATTTCATGAAGCAAACAATCAGCAATGCCTGTGGAACAATCGGATTGATCCATGTGCTATTGCGAAC
AATAAAGACAAGATGCACTTTGAATCTGGATCAACCTTGAAAAAAATTCCTGGAAGAGTCTGTGTCAATGAGCCCTGAAG
AATGAGCCAAGTACTTGGAGAACTATGACGCCATTCAAGTGACTCATGAGACCAGTGCCCACGAAGGTCAGACTGAGGCA
TCAAATATAGATGAAAAAGTAGATCTTCATTTTATTGCATTAGTTCATGTAGATGGGCATCTCTATGAATTAGATGGGCG
GAAACCATTTCCAATTAACCATGGAAAAACTAGTGATGAAAGTTTATTAGAGGATGCCATAGAAGTTTGCAAGAAGTTTA
CGGAACGTGACCCTGATGAATTAAGATTTAATGTGATCACTCTTTCTGCAGCA

Alignment

ORF - retro_ocun_382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.18 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEE
          MEGQR.LPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEE
Retrocopy MEGQR*LPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEE

Parental  EKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANN-KDKMHFESGSTLKKFLEESVSMSPEERAKYLE
          EKIKSQGQDVTSSVYFMKQTISNACGTIGLIH......K...........KKFLEESVSMSPEE.AKYLE
Retrocopy EKIKSQGQDVTSSVYFMKQTISNACGTIGLIHVLLRTIKTRCTLNLDQP*KKFLEESVSMSPEE*AKYLE

Parental  NYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDETLLEDAIEVC
          NYDAI.VTHETSAHEGQTEA.NIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDE.LLEDAIEVC
Retrocopy NYDAIQVTHETSAHEGQTEASNIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDESLLEDAIEVC

Parental  KKFMERDPDELRFNAIALSAA
          KKF.ERDPDELRFN.I.LSAA
Retrocopy KKFTERDPDELRFNVITLSAA

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	0.94 RPM	19.98 RPM
SRP017611_kidney	0.30 RPM	12.97 RPM
SRP017611_liver	0.46 RPM	6.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_382 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_382 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177,
Oryctolagus cuniculus	ENSOCUG00000001353	1 retrocopy	retro_ocun_309,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382 ,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227,