RetrogeneDB ID: retro_ocun_925

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:80015490..80016188(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCNM1
• Ensembl ID: ENSOCUG00000026766
• Aliases: None
• Description: sodium channel modifier 1 (SCNM1), mRNA [Source:RefSeq mRNA;Acc:NM_001171298]

Sequence

>retro_ocun_925
ATGTCTTCCAAGAGAGAAGGGGATGATTGGAGTCAGCTCAATGCGCTCTCATCAAAAAAAAAATAAAGGAGAGTGGGAGA
CCTGTTGGCCAGTTACATCCCGGAAGATGAGGCGATGATGTTACAGGATGGATGCTTTGCATGTGCCATCTGCCCTCACT
GACCTGTCCTGGACGCCCTGGCCATGCTGAAGGCCCACCGTGCAGGCAAGACACATCTGTCCAACCTGCAGCTTTTCTAT
GGAAAGAAACAGCCAGGAAAGGACATGGAGCAAAATTCAAAAGAGCAGAATGAATCGAGGGAAGAGACCAAAGTTGAAGC
TCCTCTGCTAACCTAGATTCGCCTTATCACCCAGAGTGCTCTGCACAGAGCTCCCCACCATAACAGTTGCTGCTGCTGCA
AGTACAGACCAGAAGTTCCTGGTTCCTCTGTCTCTCGTTCTGCTTTGCCATCAGCTGCAGAGCTGGAACTCCAAAGTGGG
AAAATCAGTAGGGAACCTGAGAGTGCGGCTGACCCACAGGCCAAGGAGTCAGCAATTGTCTCAGCCCCTGCACCCATGAG
CCCCTCAAGAAGATGAGCCCTGGATCACTACCTCACTCTTCAAAGCTCTGGATGGATCCCAGATGAAGAGGTCGATGGGT
AAAAGATGAAAATGTTGAGTTTGACTCTGATGAAGAACCACTTGACCTGCCCCTGGAC

Alignment

ORF - retro_ocun_925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSFKREGDDWSQLNVL----KKRRVGDLLASYIPEDEALMLRDGRFACAICPHRPVLDTLAMLTAHRAGK
          MS.KREGDDWSQLN.L....K.RRVGDLLASYIPEDEA.ML.DG.FACAICPH.PVLD.LAML.AHRAGK
Retrocopy MSSKREGDDWSQLNALSSKKK*RRVGDLLASYIPEDEAMMLQDGCFACAICPH*PVLDALAMLKAHRAGK

Parental  KHLSSLQLFYGKKQPGKDVEQNPRQQNESREETTVEAPLLTQTRLITQSALHRAPHYNSCCRRKYRCVGR
          .HLS.LQLFYGKKQPGKD.EQN...QNESREET.VEAPLLT..RLITQSALHRAPH.NSCC..KYR....
Retrocopy THLSNLQLFYGKKQPGKDMEQNSKEQNESREETKVEAPLLT*IRLITQSALHRAPHHNSCCCCKYRPEVP

Parental  ERQVSRSPLPSAAELELQSGKISREPESAADPQAKESATVSAPAPMSPSRRRALDHYLTLRSSGWIPDG-
          ...VSRS.LPSAAELELQSGKISREPESAADPQAKESA.VSAPAPMSPSRR.ALDHYLTL.SSGWIPD..
Retrocopy GSSVSRSALPSAAELELQSGKISREPESAADPQAKESAIVSAPAPMSPSRR*ALDHYLTLQSSGWIPDE<

Parental  RGRWVKDENVEFDSDEEEPPDLPLD
          RGRWVKDENVEFDSD.EEP.DLPLD
Retrocopy RGRWVKDENVEFDSD-EEPLDLPLD

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	14.68 RPM
SRP017611_kidney	0.10 RPM	13.48 RPM
SRP017611_liver	0.00 RPM	4.47 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_925 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_925 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_925 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004323	1 retrocopy	retro_dnov_1019,
Oryctolagus cuniculus	ENSOCUG00000026766	1 retrocopy	retro_ocun_925 ,
Rattus norvegicus	ENSRNOG00000021092	1 retrocopy	retro_rnor_2550,