RetrogeneDB ID: retro_ocun_1732

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018828:422990..423677(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000004798
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSOCUG00000015964
• Aliases: None
• Description: beclin 1, autophagy related [Source:HGNC Symbol;Acc:1034]

Sequence

>retro_ocun_1732
TTGGAGGGGTCCAAGACGCCCAGCAGCACCATGCAGGTGAGCTTTGTGTGCCAGCGCTGCAGCCAGCCCCTCAAGCTGGA
CACGAGCTTCAAGATCCTGGACCGGGTCACCATCCAGGAGCTCACAGCTCCATTACTTGCCACAGCCCAGGTCAAACCAG
GAGACCCCCAGGAGGAAGAGGCTAACTCAGGAGAGGAAGCATTTATTGAAACTCGCCAGGATGGTTTCTCTCGCAGATTC
ATGCCCCCAGCCAGGGTGATGTCTACAGAAAGTGCCAACAGCTTCACTCTGATCAGGGAGGCGTCCGACAGCAGCACCAT
GGAGAACCTCAGCCGAAGACTGAAGGTCACTGGGGACCTTTTTGACATCATGTCGGGCCAGACAGACGTGGATCACCCAC
TGTGTGAGGAATGCACGGATACTCTCTTAGACCAGCTGGACACTCAGCTCCATGTCACCGAAAATGAGTGTCAGAACTAC
AAGCGCTGTTTGGAGATCTTGGAGCAGATGAACGAGGTTGACAGTGAGCAACTGCAGAAGGAGCTGAGGGAGCTGGCCCT
GGAGGAGGAACGGCTGGTCCAGGAACTGGAAGATGTGGAAAAGAACCGCAGAACGGTGGCAGAAAACCTGGAGAAGGTCC
AGGCTGAGGCTGAGTGGCTGGATCAGGAGGAAGCTCAGTATCAGAGA

Alignment

ORF - retro_ocun_1732 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.63 %
• Parental protein coverage: 52.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEGSKTPSSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLATAQVKPGDPQEEEANSGEEAFIE
          .EGSKTPSSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLATAQVKPGDPQEEEANSGEEAFIE
Retrocopy LEGSKTPSSTMQVSFVCQRCSQPLKLDTSFKILDRVTIQELTAPLLATAQVKPGDPQEEEANSGEEAFIE

Parental  TRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTD
          TRQDG.SRRF.PPAR.MSTESANSFTLI.EASD..TMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTD
Retrocopy TRQDGFSRRFMPPARVMSTESANSFTLIREASDSSTMENLSRRLKVTGDLFDIMSGQTDVDHPLCEECTD

Parental  TLLDQLDTQLHVTENECQNYKRCLEILEQMNEDDSEQLQKELRELALEEERLVQELEDVEKNRRTVAESL
          TLLDQLDTQLHVTENECQNYKRCLEILEQMNE.DSEQLQKELRELALEEERLVQELEDVEKNRRTVAE.L
Retrocopy TLLDQLDTQLHVTENECQNYKRCLEILEQMNEVDSEQLQKELRELALEEERLVQELEDVEKNRRTVAENL

Parental  EKVQAEAERLDQEEAQYQR
          EKVQAEAE.LDQEEAQYQR
Retrocopy EKVQAEAEWLDQEEAQYQR

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	0.61 RPM	43.65 RPM
SRP017611_kidney	1.01 RPM	49.77 RPM
SRP017611_liver	0.23 RPM	24.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1732 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1732 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732 , retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,