RetrogeneDB ID: retro_ocun_472

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:44411945..44412525(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOLR1
• Ensembl ID: ENSOCUG00000000165
• Aliases: None
• Description: folate receptor 1 (adult) [Source:HGNC Symbol;Acc:3791]

Sequence

>retro_ocun_472
GCATGTACCAACAAGTACCACATGGAAAGGCCAAGCACTGGGACAAGTTATATGAGCAGATTCAACTAGGACCACTGTGG
CAAGATGGAGCCTGCCTACAAGCATCACTTTGTCCAGGACACCTGCCTCTGTGAGTGCTCCCCCAATCTGGGGCCCTGGA
TCCAACAGGTGGACCAGAGCTGCAGCAAAGAGCAGATCCTGAATGTGCCCCTGTGCAAAGAGGATTGTTAGCACTGGTGG
GAGGACTGTCACAACTCCAGAACCTGCAAGAGCAATTTTTGGCACAAGGGCTAGAACTGGAACTTGGGATTTAACCAGTG
CCCAGTGGGAGCTGCCTGCCACCCTTTCTGCTCTAGTTCCCTACACGTGCTGCTCTGTGTGAAGAAATCTGGAGTTACTC
CTACAAGGCTAGCAACTGCAGCCTTGGGAACAGCCACTGCCTTCAGATGTGGTCCAGGTTGGCCCAGGGCAACCCCAATG
AGGAGATGGGTAGGTTCTATACTGAGGCCATGAGTGGGGCTAGGATCCAGGGGGCCTGGCCTCTCTTGCCCAGTCTGGCC
CCTTGATGCTCTTTCTGCTC

Alignment

ORF - retro_ocun_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.39 %
• Parental protein coverage: 75.39 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ACCSTNTSQEAHKDISYLYRFNWDHCGKMEPACKRHFIQDTCLYECSPNLGPWIQQVDQSWRKERVLDVP
          AC.............SY..RFN.DHCGKMEPA.K.HF.QDTCL.ECSPNLGPWIQQVDQS..KE..L.VP
Retrocopy ACTNKYHMERPSTGTSYMSRFN*DHCGKMEPAYKHHFVQDTCLCECSPNLGPWIQQVDQSCSKEQILNVP

Parental  LCKEDCQRWWEDCRTSHTCKSN-WHKGWNWTSGFNQCPVGAACHP-FHFYFPTPAALCEEIWSHSYKASN
          LCKEDC..WWEDC..S.TCKSN.WHKG.NW..GFNQCPVGAACHP.F...FPT.AALCEEIWS.SYKASN
Retrocopy LCKEDC*HWWEDCHNSRTCKSNFWHKG*NWNLGFNQCPVGAACHP<FLL*FPTRAALCEEIWSYSYKASN

Parental  YSRGSGRCIQMWFDPAQGNPNEEVARFYAEAMSEAALHRAWPLLPSLV-PLLLFLL
          .S.G...C.QMW...AQGNPNEE..RFY.EAMS.A....AWPLLPSL..PL.LFLL
Retrocopy CSLGNSHCLQMWSRLAQGNPNEEMGRFYTEAMSGARIQGAWPLLPSLA<PLMLFLL

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	3.92 RPM
SRP017611_kidney	0.00 RPM	352.32 RPM
SRP017611_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_472 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_472 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005777	1 retrocopy	retro_cfam_1723,
Callithrix jacchus	ENSCJAG00000015224	1 retrocopy	retro_cjac_3330,
Dasypus novemcinctus	ENSDNOG00000000856	1 retrocopy	retro_dnov_1751,
Echinops telfairi	ENSETEG00000015365	2 retrocopies	retro_etel_1160, retro_etel_128,
Myotis lucifugus	ENSMLUG00000014126	2 retrocopies	retro_mluc_1199, retro_mluc_567,
Monodelphis domestica	ENSMODG00000008017	1 retrocopy	retro_mdom_990,
Monodelphis domestica	ENSMODG00000008032	1 retrocopy	retro_mdom_588,
Monodelphis domestica	ENSMODG00000008042	1 retrocopy	retro_mdom_648,
Mus musculus	ENSMUSG00000001827	1 retrocopy	retro_mmus_1438,
Oryctolagus cuniculus	ENSOCUG00000000165	1 retrocopy	retro_ocun_472 ,
Otolemur garnettii	ENSOGAG00000000641	5 retrocopies	retro_ogar_2539, retro_ogar_2666, retro_ogar_2758, retro_ogar_2908, retro_ogar_532,
Tarsius syrichta	ENSTSYG00000003503	3 retrocopies	retro_tsyr_1057, retro_tsyr_111, retro_tsyr_1651,