RetrogeneDB ID: retro_ocun_452

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:63960467..63960671(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000026246
• Aliases: None
• Description: None

Sequence

>retro_ocun_452
ATGTCCAAGAAAAAGCACCTGGTAAACTTAGGTCTCCTAGAGGAGGACGAAGACAAGTTCAAGGTGTTCCCTGCAATAGA
CCGGGCTGGTTTAGATGAAGATGCACATGTCTGGGAGGATAATTGGGATGGTGATAACATGGAGCATGACTTCTCCAATC
AGTTATGAGCTGAACTGGAGAAGCATGGTTATGAGACTGAGACT

Alignment

ORF - retro_ocun_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 98.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSEKKQPVDLGLLEED-DEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDDFSNQLRAELEKHGYKMET
          MS.KK..V.LGLLEED.D.F..FPA.D.AGL..DEDAHVWEDNWD.DN.E.DFSNQL.AELEKHGY..ET
Retrocopy MSKKKHLVNLGLLEEDEDKFKVFPAIDRAGL--DEDAHVWEDNWDGDNMEHDFSNQL*AELEKHGYETET

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	35.71 RPM
SRP017611_kidney	0.00 RPM	46.62 RPM
SRP017611_liver	0.08 RPM	18.04 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_452 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010434	1 retrocopy	retro_amel_1234,
Canis familiaris	ENSCAFG00000002179	1 retrocopy	retro_cfam_1174,
Cavia porcellus	ENSCPOG00000010402	1 retrocopy	retro_cpor_446,
Equus caballus	ENSECAG00000018179	1 retrocopy	retro_ecab_360,
Erinaceus europaeus	ENSEEUG00000002237	2 retrocopies	retro_eeur_290, retro_eeur_586,
Echinops telfairi	ENSETEG00000019778	1 retrocopy	retro_etel_961,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452 , retro_ocun_77,
Sus scrofa	ENSSSCG00000015337	1 retrocopy	retro_sscr_67,
Ictidomys tridecemlineatus	ENSSTOG00000011501	1 retrocopy	retro_itri_253,
Tupaia belangeri	ENSTBEG00000016474	3 retrocopies	retro_tbel_2837, retro_tbel_2998, retro_tbel_3844,