RetrogeneDB ID: retro_ocun_1466

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:18347968..18348634(+)
• Located in intron of: ENSOCUG00000010286

Retrocopy information

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

Parental gene information

• Parental gene symbol: MARC2
• Ensembl ID: ENSOCUG00000013162
• Aliases: None
• Description: mitochondrial amidoxime reducing component 2 [Source:HGNC Symbol;Acc:26064]

Sequence

>retro_ocun_1466
GTCTCCATCTTCTATGAGAAAAACAGCCTGATCTTCAGCGCTCCGGGGATGGACCAGCTGGTGTTACCCAGCAGGCTGCC
TTCCACCAACACACTCCATGACTGCAGAATATTCGGTGTTGACATCCAAGGCAGAGACTGTGGTGACGAGGTCGCTCAGT
GGTTCACCAACTTCTTGAAAACGGAAGCATTGAGGTTGGTTCAGTTTGACACGAAGATGAAGGGAAGAACATCGAACAAA
CTTTTCCCTGTTTCTGTACAGAATTACCAGGTGGCCTATCCAGACTGCAGCCCACTCATGATCCTCTCAGAAGCCTCCCT
GGGGGATCTGAATATGAGGCTGGAGAAGAAAATCAAGATGGAGCAATTCAGGCCCAACATCGTGGTGAGGGGCTGTGAGG
CCTACGAGGAGGATACCTGGGATGAACTCCTCATTGGTGGGGTAGAACTGAAAAAGGTATTAGCTTGCCCCAGGTGCATT
TTGACCACTGTGGACCCAGATACAGGAGTCATAGATAGGAAGGAGTCCCTGGAAACACTGGAGAGCTACTGCTTGTGTGA
TGCTTCTGAGCATCACATATACAAGTCATCCCCACTTTTTGGAATGTATTATTCAGTGGAAAAAATAGGAAGCCTGAGAG
TTGGTGACTCTGTGTATCGGATGGTG

Alignment

ORF - retro_ocun_1466 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.14 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSISYEKNSLIFSAPGMDQLVLPSRPPSTNTLHDCRIFGVDIQGRDCGDEVAQWFTNFLKTEALRLVQFD
          VSI.YEKNSLIFSAPGMDQLVLPSR.PSTNTLHDCRIFGVDIQGRDCGDEVAQWFTNFLKTEALRLVQFD
Retrocopy VSIFYEKNSLIFSAPGMDQLVLPSRLPSTNTLHDCRIFGVDIQGRDCGDEVAQWFTNFLKTEALRLVQFD

Parental  TKLKGRTSDKLFPVSVQNYQVAYPDCSPLMIISEASLGDLNTRLEKKIKMEQFRPNIVVRGCEAYEEDTW
          TK.KGRTS.KLFPVSVQNYQVAYPDCSPLMI.SEASLGDLN.RLEKKIKMEQFRPNIVVRGCEAYEEDTW
Retrocopy TKMKGRTSNKLFPVSVQNYQVAYPDCSPLMILSEASLGDLNMRLEKKIKMEQFRPNIVVRGCEAYEEDTW

Parental  DELLIGGVELKKVLACPRCILTTVDPDTGVIDRKEPLETLKSYRLCDPSEHHIYKSSPLFGMYYSVEKIG
          DELLIGGVELKKVLACPRCILTTVDPDTGVIDRKE.LETL.SY.LCD.SEHHIYKSSPLFGMYYSVEKIG
Retrocopy DELLIGGVELKKVLACPRCILTTVDPDTGVIDRKESLETLESYCLCDASEHHIYKSSPLFGMYYSVEKIG

Parental  SLKVGDPVYRLV
          SL.VGD.VYR.V
Retrocopy SLRVGDSVYRMV

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	0.00 RPM	109.16 RPM
SRP017611_kidney	0.00 RPM	376.34 RPM
SRP017611_liver	0.08 RPM	361.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1466 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1466 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011332	1 retrocopy	retro_cfam_469,
Oryctolagus cuniculus	ENSOCUG00000013162	1 retrocopy	retro_ocun_1466 ,
Rattus norvegicus	ENSRNOG00000037850	1 retrocopy	retro_rnor_162,
Ictidomys tridecemlineatus	ENSSTOG00000006676	1 retrocopy	retro_itri_1413,