RetrogeneDB ID: retro_ocun_296

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:104442125..104442482(+)
• Located in intron of: ENSOCUG00000012919

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSA
• Ensembl ID: ENSOCUG00000003267
• Aliases: None
• Description: endosulfine alpha [Source:HGNC Symbol;Acc:3360]

Sequence

>retro_ocun_296
ATGTCCCAGAAACAAGAGAACCCTGCTGAGGAGACCGGCGAGAAGAAGCAGGACACACAAGAGAAAGAAGGTATTCTCCC
TGAAGGAGCTGAGAAAGCAAAGCTAAAGGCCAAATAGCCAAGCCTAGGGCGAAAGCCCGGAGGCTCTGACTTCCTCGTGA
AGAGGCTCCAGAAAGAGCAAAAGTACCTTGACTCAGGAGACCGCAACATGGCCAAAGCCAAGATGAAGAATAAGCAGCTG
CCAAGGGCAGGACAAGACAAGAACCTGGTGACTGGTGACCACATCCCCACCCCACAGGATCTGCCCCAGGGAAAGTCCTC
ACTCAACACCTGCAAGCTTGCCGGTGGCCAAGTTGAA

Alignment

ORF - retro_ocun_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSQKQEDENPAEETGEEKQDTQEKEGILPERAEEAKLKAKYPSLGQKPGGSDFLMKRLQKGQKYFDSGDY
          MSQKQE..NPAEETGE.KQDTQEKEGILPE.AE.AKLKAK.PSLG.KPGGSDFL.KRLQK.QKY.DSGD.
Retrocopy MSQKQE--NPAEETGEKKQDTQEKEGILPEGAEKAKLKAK*PSLGRKPGGSDFLVKRLQKEQKYLDSGDR

Parental  NMAKAKMKNKQLPSAGPDKNLVTGDHIPTPQDLPQRKSSLVTSKLAGGQVE
          NMAKAKMKNKQLP.AG.DKNLVTGDHIPTPQDLPQ.KSSL.T.KLAGGQVE
Retrocopy NMAKAKMKNKQLPRAGQDKNLVTGDHIPTPQDLPQGKSSLNTCKLAGGQVE

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	37.42 RPM
SRP017611_kidney	0.20 RPM	14.39 RPM
SRP017611_liver	0.00 RPM	6.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_296 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000143420	3 retrocopies	retro_hsap_1449, retro_hsap_2208, retro_hsap_2452,
Mus musculus	ENSMUSG00000038619	1 retrocopy	retro_mmus_2675,
Oryctolagus cuniculus	ENSOCUG00000003267	3 retrocopies	retro_ocun_296 , retro_ocun_396, retro_ocun_722,
Oryctolagus cuniculus	ENSOCUG00000015489	10 retrocopies	retro_ocun_1182, retro_ocun_1297, retro_ocun_1398, retro_ocun_1573, retro_ocun_1731, retro_ocun_1768, retro_ocun_310, retro_ocun_473, retro_ocun_479, retro_ocun_698,
Otolemur garnettii	ENSOGAG00000005863	3 retrocopies	retro_ogar_1769, retro_ogar_1911, retro_ogar_2262,
Pongo abelii	ENSPPYG00000000893	2 retrocopies	retro_pabe_1803, retro_pabe_2081,
Rattus norvegicus	ENSRNOG00000048617	1 retrocopy	retro_rnor_1776,