RetrogeneDB ID: retro_ocun_1022

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 19:36304460..36304786(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNX3
• Ensembl ID: ENSOCUG00000005858
• Aliases: None
• Description: sorting nexin 3 (SNX3), mRNA [Source:RefSeq mRNA;Acc:NM_001171324]

Sequence

>retro_ocun_1022
GTCAAGACAAGTCTTCCAATTTTCAAGCTGAAGGAATCTACCGTTAGAAGAAGATACAGTGACTTTGAATGACTGTGAAG
TGAATTAGAGAGAGCAAGGTTGTAGTTCCCCCACTCCCTGGGAAAGCATTTTTGCGCCAACTTCCTTTTAGAGGAGATGA
CGGAATATTTGATGACAATTTTATTGAGGAAAGGAAGCAAGGACTGGAGCAGTTTATAAACAAGGTCGCTGGTCATCCTC
TGGCACAGAATGAACGTTGTCTTCACATGTTTTTACAGGATGAAATCATAGATAAAAGGTATACTCCCTCTAAAATAAGG
TATGCC

Alignment

ORF - retro_ocun_1022 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.09 %
• Parental protein coverage: 67.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKTNLPIFKLKESTVRRRYSDFEWLRSELER-ESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQG
          VKT.LPIFKLKESTVRRRYSDFE.L.SELER....VV.P.LPGKAFLRQLPFRGDDGIFDDNFIEERKQG
Retrocopy VKTSLPIFKLKESTVRRRYSDFE*L*SELER<SKVVVPP-LPGKAFLRQLPFRGDDGIFDDNFIEERKQG

Parental  LEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA
          LEQFINKVAGHPLAQNERCLHMFLQDEIIDK.YTPSKIR.A
Retrocopy LEQFINKVAGHPLAQNERCLHMFLQDEIIDKRYTPSKIRYA

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	0.44 RPM	153.87 RPM
SRP017611_kidney	0.51 RPM	131.56 RPM
SRP017611_liver	0.00 RPM	39.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1022 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1022 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1022 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015256	1 retrocopy	retro_eeur_525,
Echinops telfairi	ENSETEG00000003537	3 retrocopies	retro_etel_1331, retro_etel_645, retro_etel_924,
Felis catus	ENSFCAG00000024997	1 retrocopy	retro_fcat_1705,
Loxodonta africana	ENSLAFG00000018131	1 retrocopy	retro_lafr_579,
Oryctolagus cuniculus	ENSOCUG00000004744	1 retrocopy	retro_ocun_918,
Oryctolagus cuniculus	ENSOCUG00000005858	2 retrocopies	retro_ocun_1022 , retro_ocun_750,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Tupaia belangeri	ENSTBEG00000011755	3 retrocopies	retro_tbel_2964, retro_tbel_3503, retro_tbel_3929,
Tursiops truncatus	ENSTTRG00000008868	2 retrocopies	retro_ttru_1028, retro_ttru_1103,