RetrogeneDB ID: retro_ocun_269

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:3804628..3805102(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S5
• Ensembl ID: ENSOCUG00000025755
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 5, muted [Source:HGNC Symbol;Acc:18561]

Sequence

>retro_ocun_269
GGTTGTGAGGTCCCCCCGGATGGCGGCAGCAAGAATCGGGACTTGCTGGGGACCACAGGCTCAGCACATCTCATTATCAA
GGATCTTGGAGAAATTCATTTGAGACTTTTGGATCACAGACCAGTTATTCAAGGAGAAACTCGTTATTTTGTAAAAGAAT
TTGAAGAAAAACATGGTCTTCAGGAAATGTGAGTTCTTGAAAATCTGAAGAATATGATCCATGAAGCAAATGAACACACT
CTTCCCAAACATAGAGAAACAGTGCAGGACAACTTAAAGCAAGCCCTCCAGAGATTGCAAGCGGCCAGTTACTCAGTCTG
TAGACTCCAACAGAGAGAACAGGAACGGAGAAAGATGTATAATGACCATTTAGTAGCTAATGAGAAGCAGCACCTCCTCC
AGTGGGAAGATTTCACGAAAGAACAACCCCAGAAGTGGGCAGAAGTGGGGGAAGCTGTGGAGAGGCTGAACGAG

Alignment

ORF - retro_ocun_269 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 86.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCEVPTGGGGKKRDSLGTAGSAHLIIKDLGEIHSRLLDHRPVIQGETRYFVKEFEEKRGLREMRVLENLK
          GCEVP..GG.K.RD.LGT.GSAHLIIKDLGEIH.RLLDHRPVIQGETRYFVKEFEEK.GL.EM.VLENLK
Retrocopy GCEVPPDGGSKNRDLLGTTGSAHLIIKDLGEIHLRLLDHRPVIQGETRYFVKEFEEKHGLQEM*VLENLK

Parental  NMIHETNEHTLPKCRETMQDNLQQVLQRLQAANDSVCRLQQREQERKKMYNDRLVANEKRRSLQWEEFMK
          NMIHE.NEHTLPK.RET.QDNL.Q.LQRLQAA..SVCRLQQREQER.KMYND.LVANEK...LQWE.F.K
Retrocopy NMIHEANEHTLPKHRETVQDNLKQALQRLQAASYSVCRLQQREQERRKMYNDHLVANEKQHLLQWEDFTK

Parental  EQPQKRAAVDEEHRKAVARLRE
          EQPQK.A.V.E....AV.RL.E
Retrocopy EQPQKWAEVGE----AVERLNE

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	3.64 RPM
SRP017611_kidney	0.00 RPM	10.85 RPM
SRP017611_liver	0.08 RPM	3.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_269 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_269 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_269 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699, retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269 ,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179, retro_itri_1901,