RetrogeneDB ID: retro_ocun_218

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:25468401..25469697(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000017468
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_218
AGACCCAAGGTTAAAGTCAAGACCTCTGCCATGTCTCCTATCTTCATCTGCCAGCGTTGCAGCCAGCCGCTGAAACTGAG
CGAGCCCCTGGAGATGCTGGCCTCAACACAGGGGGAGCAAGGAGAGAGCCAGGAAACCGGCACCTCCTCCGAAAAGATGA
GAGGGAGTGAAAAACTACAGGTGGGTGCCTCCGGAGGAGCCCTTCCCGAAGACAGCAACACATCGGAGGACAGCGGCGGC
TTCACCCTGCTTGGGGACGTTTGCTCCGTGGGAACCTTGAGTAGCCTCCAAGAGGCCACCGTGCAGATTTTTGACATCCT
CTCCGGGCAGAAAGATGTGGAGCATCCACTGTGTGAGGAGTGTACCGACAACCTCCTGGAGCAGCTGGACTCCCAGCTCA
CCCTCGTCGAACTTGACACTCAGAACTACAAACGCTGCCTGGAGTCTGGGGAGCTGCAGGTGGAGCCTGAGACCGAGTCG
CTGCAGGCGGAGCTGCGGGCCCTGGAACTGGAGGAGGCCCGGCTGGCCCGGGAGCTGGAGGACGTGGACAAGGGCTGTGC
GAGGGTAGCAGCGGCTCTCCAGGAGGCCGAGGCAGAGACACAGGAGCTGGAGCAGCGGGAGAGGCAGTCCCACAGGGAGT
ACAGTGCGCTGAAGTGGCAGCAGCTGGAGCTGTGTGACCAGCTGGGGAGCATAGAGAATCAGCTGTGGTACGCCCAGGCG
CAGCTGCACTGGCTGAATAAAACCAGCATCTTCCAAGTCACGTTTGAAATCCGGGAGGAGGGCTCCGTGGGCATCATCAA
CAACCTCCGCTTGGGCTGCCTCCCCATCGGCCCTGTGGACTGGAACGAGATCAACGCTGCCTGGGGACAGGTGGCCTTGC
TGCTGCTCGCTCTGTCCAACACAATTGGCCTGGAGTTCCAGAGGTACCAGCTCATCCCTTGCGCAGACCACTCCTATCTG
AAGCCTTTGACAGGTAACTCGGCTCTGCTACCCTTGTTCTCTGATGGGAGCCAGAATGTTTTCCTGAGCAACAAGTTCGA
CCGCGCCATGATTGCCTTCCTGGACTGCTTGCAGCAGTTCAAGGAAAAGGCCGAGAAAGGGAAGCAGGGCCTTCGGCTGC
CCTACAGGATCCGAGTAGAGGAAGGCCTGCTGGAGGACTCCACAGGCAGTGGGGAATGCTGTGCCCTCAGGAGCCATCTG
AACACCAGGGAGCAGTGGACACGGGCGCTCAAATTCATGCTTGTCAATTTGAAATGTAGCCTTGCTTGGGCCTCCTTAAG
ATATCGTAAAAGTTAA

Alignment

ORF - retro_ocun_218 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.57 %
• Parental protein coverage: 87.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLATAQVKPGDPQEEEANSGEEAFIETRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLSRRL
          .LA..Q...G..QE....S......E..Q.G.S....P.....S.E....FTL.G.....GT...L....
Retrocopy MLASTQGEQGESQETGTSSEKMRGSEKLQVGASGGALPEDSNTS-EDSGGFTLLGDVCSVGTLSSLQ---

Parental  KVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLHVTENECQNYKRCLEILEQMNEDDSEQLQKELRE
          ..T...FDI.SGQ.DV.HPLCEECTD.LL.QLD.QL...E...QNYKRCLE..E...E...E.LQ.ELR.
Retrocopy EATVQIFDILSGQKDVEHPLCEECTDNLLEQLDSQLTLVELDTQNYKRCLESGELQVEPETESLQAELRA

Parental  LALEEERLVQELEDVEKNRRTVAESLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVENQMRY
          L.LEE.RL..ELEDV.K....VA..L....AE...L.Q.E.Q..REYS..K.QQLEL.D.L.S.ENQ..Y
Retrocopy LELEEARLARELEDVDKGCARVAAALQEAEAETQELEQRERQSHREYSALKWQQLELCDQLGSIENQLWY

Parental  AQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMGLKFQ
          AQ.QL..L.KT..F..TF.I...G..G.INN.RLG.LP..PV.WNEINAAWGQ..LLL.AL.N..GL.FQ
Retrocopy AQAQLHWLNKTSIFQVTFEIREEGSVGIINNLRLGCLPIGPVDWNEINAAWGQVALLLLALSNTIGLEFQ

Parental  RYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCLPYRM
          RY.L.P...HSYL..LT..S..LPL...G....F..NKFD.AM.AFLDC.QQFKE..EKG.....LPYR.
Retrocopy RYQLIPCADHSYLKPLTGNSALLPLFSDGSQNVFLSNKFDRAMIAFLDCLQQFKEKAEKGKQGLRLPYRI

Parental  DVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKA
          .VE.G..ED..GSG.........N..EQWT.A
Retrocopy RVEEGLLEDSTGSGECCALRSHLNTREQWTRA

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	43.65 RPM
SRP017611_kidney	0.00 RPM	49.77 RPM
SRP017611_liver	0.00 RPM	24.12 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_218 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_218 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,