RetrogeneDB ID: retro_ocun_1542

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: AAGW02082071:8253..8429(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SERP1
• Ensembl ID: ENSOCUG00000016085
• Aliases: None
• Description: stress-associated endoplasmic reticulum protein 1 [Source:HGNC Symbol;Acc:10759]

Sequence

>retro_ocun_1542
ATCCCTATGGTCAAAGAGAAGCATAGCAAGAATGTCATCAGGGGTAGTAGCTTTGCCAAGACCTCAAAAAATGAGCTCAA
AGAGAAGGAATCTGTAGGACTGGTTATTGGTGCTCTTCATTTTCTTGTTTGTTGCTGTGCAACTCTCCAAATTATTCAAG
TATCTTGATGGGTATG

Alignment

ORF - retro_ocun_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.1 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IRMANEKHSKNITQRGNVAKTSRNAPEEKASVGPWLLALFIFVVCGSAIFQIIQ-SIRMGM
          I.M..EKHSKN.......AKTS.N...EK.SVG....AL..F.VC..A..QIIQ.SI.MGM
Retrocopy IPMVKEKHSKNVIRGSSFAKTSKNELKEKESVGLVIGALH-FLVCCCATLQIIQ<SILMGM

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	11.53 RPM
SRP017611_kidney	0.00 RPM	27.67 RPM
SRP017611_liver	0.00 RPM	12.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1542 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013995	15 retrocopies	retro_dnov_1100, retro_dnov_1145, retro_dnov_1170, retro_dnov_1416, retro_dnov_1500, retro_dnov_1524, retro_dnov_1533, retro_dnov_1649, retro_dnov_1715, retro_dnov_1724, retro_dnov_1746, retro_dnov_1784, retro_dnov_1847, retro_dnov_2299, retro_dnov_856,
Microcebus murinus	ENSMICG00000000414	1 retrocopy	retro_mmur_1429,
Oryctolagus cuniculus	ENSOCUG00000016085	2 retrocopies	retro_ocun_1542 , retro_ocun_1835,