RetrogeneDB ID: retro_ocun_1507

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:50017565..50018241(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF141
• Ensembl ID: ENSOCUG00000002807
• Aliases: None
• Description: ring finger protein 141 [Source:HGNC Symbol;Acc:21159]

Sequence

>retro_ocun_1507
ATGGGACAGCAAATTTCAGATCAGACCCAACTGGTTATTAGCAAGTTACCAGAAAAAGTAGCAAAACACGTCACATTGGT
TCGAGAAAGTGGCTCCTTAACATATAAAGAATTTCTTGAGAGAGTAGCTGAACTTGGTGTAACTGCTAAAGTGGCTTCTG
GCCAGGAGAAACATCTTCTCTTTGAGGTACAACCTGGATCTGATTCCTCTGCCTTTTGGAAAGTGGTTGACGGGTAGTGT
GTACCAAGATTAACAAGAGGAGTGGCATTGTGGAAGCATCACGCATCATGAATTTGTACCAGTTCCTTCAGCTTTATAAA
GGCATCACAAGTCATGCAGCAGGTGCTTTGGCGCAAAGCACCACTTCTGAAGAACCTGAGGAAAACGCATGCTCTGTCAC
ACCTTGTCAGGCCCAGTCTTTGGATGGGAAGGGCGAAACAGCTGACCGATGAGGAGGTGTGTTATATCTGCATGGATGGG
CGGGCTGACCTCATCCTGCCTTGTGCTCACAGCTATTTGTCAGAAGTGTATAGATAAATGGAGAGACGGACACAGGAATT
GCCCTATTTGTCGCCTGCAGATGACTGGAGCAAATGAGTCTTGGGTAGCGTCAGACGCGCCTACTAAAGATGACGTACTA
AACATGGCTGATGAGGCCGACCAGCCCCATCGGCCA

Alignment

ORF - retro_ocun_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGQQISDQTQLVISKLPEKVAKHVMLVRESGSLTYEEFLGRVAELNDVTAKVASGQEKHLLFEVQPGSDS
          MGQQISDQTQLVISKLPEKVAKHV.LVRESGSLTY.EFL.RVAEL..VTAKVASGQEKHLLFEVQPGSDS
Retrocopy MGQQISDQTQLVISKLPEKVAKHVTLVRESGSLTYKEFLERVAELG-VTAKVASGQEKHLLFEVQPGSDS

Parental  SAFWKVVV-RVVCTKINKSSGIVEASRIMNLYQFLQLYKDITSQAAGVLAQSATSEEPEENASSVTSCQA
          SAFWKVV..RVVCTKINK.SGIVEASRIMNLYQFLQLYK.ITS.AAG.LAQS.TSEEPEENA.SVT.CQA
Retrocopy SAFWKVVD<RVVCTKINKRSGIVEASRIMNLYQFLQLYKGITSHAAGALAQSTTSEEPEENACSVTPCQA

Parental  -SLWMGRVKQLTDEEECCICMDGRADLILPCAHSF-CQKCIDKWSDRHRNCPICRLQMTGANESWVVSDA
          .SLWMGR.KQLTDEE.C.ICMDGRADLILPCAHS..CQKCIDKW.D.HRNCPICRLQMTGANESWV.SDA
Retrocopy >SLWMGRAKQLTDEEVCYICMDGRADLILPCAHSY>CQKCIDKWRDGHRNCPICRLQMTGANESWVASDA

Parental  PTEDDMANYILNMADEAGQPHRP
          PT.DD.....LNMADEA.QPHRP
Retrocopy PTKDD----VLNMADEADQPHRP

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	0.11 RPM	20.42 RPM
SRP017611_kidney	0.10 RPM	18.55 RPM
SRP017611_liver	0.00 RPM	1.85 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1507 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175, retro_cpor_198,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507 ,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573,