RetrogeneDB ID: retro_ocun_1746

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018838:518403..518718(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTPN
• Ensembl ID: ENSOCUG00000005642
• Aliases: None
• Description: myotrophin [Source:HGNC Symbol;Acc:15667]

Sequence

>retro_ocun_1746
GACTTGGGTGAGGTGAAAGAGTATGTGGCCAAGGGAAAAGATGTCAACAGGATACTAGAAGGTTGAAGGAAGCCTCTTCA
TAATCCAGCATATTGTGGGCAGCTTGAAGTCCTGGAATTTTTGCTGCTGAAAGGAGCAGACATCAATGCTCCAGATAAAC
ATCATATTGCCCCTCTTCTGTCTGCTGTCTATGAAGGTCATGTTTCCTGTGTGAAATTGCTTCTGTCAAAGGGTGCAGAT
AAGACTGTGAAAGGTCCAGTTGGACTGACTGCCTTTGAAGCCACTGACAACCAGGCAATCAAAGCTCTTCTCCAA

Alignment

ORF - retro_ocun_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 88.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLDEVKDYVAKGEDVNRTLEGGRKPLHYAADCGQLEILEFLLLKGADINAPDKHHITPLLSAVYEGHVSC
          DL.EVK.YVAKG.DVNR.LEG.RKPLH..A.CGQLE.LEFLLLKGADINAPDKHHI.PLLSAVYEGHVSC
Retrocopy DLGEVKEYVAKGKDVNRILEG*RKPLHNPAYCGQLEVLEFLLLKGADINAPDKHHIAPLLSAVYEGHVSC

Parental  VKLLLSKGADKTVKGPDGLTALEATDNQAIKALLQ
          VKLLLSKGADKTVKGP.GLTA.EATDNQAIKALLQ
Retrocopy VKLLLSKGADKTVKGPVGLTAFEATDNQAIKALLQ

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	33.78 RPM
SRP017611_kidney	0.00 RPM	26.66 RPM
SRP017611_liver	0.00 RPM	8.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1746 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1746 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1746 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000029544	1 retrocopy	retro_lafr_924,
Monodelphis domestica	ENSMODG00000013977	4 retrocopies	retro_mdom_132, retro_mdom_165, retro_mdom_1731, retro_mdom_247,
Oryctolagus cuniculus	ENSOCUG00000005642	4 retrocopies	retro_ocun_1746 , retro_ocun_1830, retro_ocun_244, retro_ocun_993,
Drosophila melanogaster	FBgn0051715	1 retrocopy	retro_dmel_34,