RetrogeneDB ID: retro_ocun_1187

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:28569142..28570021(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021792
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TOM1L1
• Ensembl ID: ENSOCUG00000008462
• Aliases: None
• Description: target of myb1 (chicken)-like 1 [Source:HGNC Symbol;Acc:11983]

Sequence

>retro_ocun_1187
ATGGCGTTTGGGAAGAGTCACCGGGATCCTTATGCCACCTCCGTGGGCCACCTCATAGAAAAGGCTACATTTGCTGGTAT
CCAAACTGAAGATTGGGGTCAGTTCATGCACATCTGTGACATCATTAACACCACCCAGGAAGGGCCAAAAGATGCAGTAA
AAGCTTTGAAGAAAAGGATATCCAAAAACTACAATCATAAAGCAATCCAACTTACCTTGTCACTTATAGACATGTGCATG
CAGAACTGTGGTCCAAGTTTCCAATCTCTGATTGTGAAGAAAGAATTCATTAAAGATAGTCTAGTTAAGCTGCTGAATCC
CAGATACAATTTGCCATTAGACATTCAGAATCGAATCTTGAATTTCATTAAGACGTGGTCACAGGGTTTCCCAGGAGGTG
TGGATCTAACTGAAGTGAAAGAAGTGTACCTTGATCTGCTTAAGAAGGGTGTTCAGTTTCCTCCCTCAGATGCAGAGGCT
CAAAGTGCCCGACAGGAGTCTGCTCCAGTTTCATCACATCTGTCAGCATCTGTCCCCACTGCACCAGCTCTTTCTCCTGT
AGTTGCTCCCAGGAACACGACTATTACGTTAGTCCCAGAGCAGATTGGAAAACTGCACAGTGAATTGGATATGGTGAAAA
TGAATGTGAGAGTGATGCTCGACATATTGTTGGAGAATACTCCTGGATCCGAAAATCAAGAAGACGTAGAACTTCTGCAG
AAACTTTATAAGACAAGTCGGGAGATGCACAAGAGAATCATGGATCTACTTGTGGTAGTGGGAAAATGAAGATGTAACTA
TTGAGCTAATTCAAGTGAATGAGGATTTGAATAATGCCATCCTTGGATATGAGAGTTTACTCGAAATCAGCAAAGGATT

Alignment

ORF - retro_ocun_1187 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.61 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAFGKSHRDPYATSVGHLIEKATFAGLQTEDWGQFMHICDIINTTQEGPKDAVKALKKRISKNYNHKEIQ
          MAFGKSHRDPYATSVGHLIEKATFAG.QTEDWGQFMHICDIINTTQEGPKDAVKALKKRISKNYNHK.IQ
Retrocopy MAFGKSHRDPYATSVGHLIEKATFAGIQTEDWGQFMHICDIINTTQEGPKDAVKALKKRISKNYNHKAIQ

Parental  LTLSLIDMCMQNCGPSFQSLIVKKEFIKDSLVKLLNPRYNLPLDIQNRILNFIKTWSQGFPGGVDVTEVK
          LTLSLIDMCMQNCGPSFQSLIVKKEFIKDSLVKLLNPRYNLPLDIQNRILNFIKTWSQGFPGGVD.TEVK
Retrocopy LTLSLIDMCMQNCGPSFQSLIVKKEFIKDSLVKLLNPRYNLPLDIQNRILNFIKTWSQGFPGGVDLTEVK

Parental  EVYLDLLKKGVQFPPSDAEAQSARQETAPVSSHPSASVPTAPALSPVIAPRNTTITLVPEQIGKLHSELD
          EVYLDLLKKGVQFPPSDAEAQSARQE.APVSSH.SASVPTAPALSPV.APRNTTITLVPEQIGKLHSELD
Retrocopy EVYLDLLKKGVQFPPSDAEAQSARQESAPVSSHLSASVPTAPALSPVVAPRNTTITLVPEQIGKLHSELD

Parental  MVKMNVRVMFDILLENTPGSENQEDVELLQKLYKTSREMHKRIMDLLVVV-ENEDVTIELIQVNEDLNNA
          MVKMNVRVM.DILLENTPGSENQEDVELLQKLYKTSREMHKRIMDLLVVV.ENEDVTIELIQVNEDLNNA
Retrocopy MVKMNVRVMLDILLENTPGSENQEDVELLQKLYKTSREMHKRIMDLLVVV>ENEDVTIELIQVNEDLNNA

Parental  ILGYE-RFTRNQQRI
          ILGYE..FTRNQQRI
Retrocopy ILGYE<EFTRNQQRI

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	0.17 RPM	8.39 RPM
SRP017611_kidney	0.30 RPM	33.14 RPM
SRP017611_liver	0.15 RPM	33.68 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1187 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1187 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1187 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
Echinops telfairi	ENSETEG00000017657	1 retrocopy	retro_etel_1208,
Oryctolagus cuniculus	ENSOCUG00000008462	1 retrocopy	retro_ocun_1187 ,