RetrogeneDB ID: retro_ocun_1272

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 5:30467443..30468324(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026220
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM118B
• Ensembl ID: ENSOCUG00000017049
• Aliases: None
• Description: family with sequence similarity 118, member B [Source:HGNC Symbol;Acc:26110]

Sequence

>retro_ocun_1272
CAGAAGTCAAGAAAGTTTTTGAAAAGCCTCATCCGGAAACAGCCGCAGGAGCTGCTGCTGGTCATCGGGACCGGGGTCAG
CGCGGCCGTGGCCCCGGGGATCCCCGCGCTGTGCTCCTGGAGAAGCTGCATCGAGGCCGTCATCGAGGCCGCGGAGCAGC
TGGAGGTGCTGCACCCGGGGGACGTGGCCGAGTTCCGCAGGAAGGTGACGAAGGACCAGGACCTGCTGGTTGTTGCCCAC
GACCTGATCCGGAAGGTGTCCCCTCGCACGGGCGACACCAAGCCCAACTTCTTCCAGGACTGCCTGATGGAGGTCTTCGA
CAGCCTGGAGCAGTACATCCAGAACCCTGCGGTGCTGCAGTCCATCCTCAGCCTGATGGACCGGGGCACCATGGTGCTGA
CCACCAACTACGACAACCTGCTGGAGCTCTTCGGGCAGCAGCAGAACAAGCCCATGGAGTCCCTGGACCTGAAGGACAAG
ACAAAGGTCCTCCAGTGGGCAAGAGGCCACGTGAAGTACGGGGTCTGCACATTCACGGCTTGTACACGGACCCCTGTGGG
ATGGTGCTGGACCCATCGGGCTACAAGGATGTCACCCAGGACCCAGAAGTGATGGAAGTCCTGCAGAACTTGTACCGCAC
CAAGTCCTTCCTGTTCGTGGGCTGCGGGGAGACCCTCCGTGACCAGATCTTCCAGGCCCTGTTCCTCTACTCGGTGCCGG
ACAAGGTGGACCTGGAGCACTACATGCTGGTGCTCAAGGAGGACGAGGACCACTTCTTCAAGCACCAGGCGGACATGCTG
CTGCACGGCATCAAGGTGGTGTCCTACGGGGACTGCTTCGCCCACTTCCCGGGCTACGTGCAGGACCTGGCCACGCGGAT
C

Alignment

ORF - retro_ocun_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.85 %
• Parental protein coverage: 84.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKPRKLLPSLKTKKPRELVLVIGTGISAAVAPQVPALKSWKGLIQALLDAAIDFDLLEDEESKKFQKCLH
          .K.RK.L.SL..K.P.EL.LVIGTG.SAAVAP..PAL.SW...I.A...AA.....L.......F.....
Retrocopy QKSRKFLKSLIRKQPQELLLVIGTGVSAAVAPGIPALCSWRSCIEAVIEAAEQLEVLHPGDVAEFRRKVT

Parental  EDKNLVHVAHDLIQKLSPRTSNVRSTFFKDCLYEVFDDLESKMEDSGKQLLQSVLHLMENGALVLTTNFD
          .D..L..VAHDLI.K.SPRT......FF.DCL.EVFD.LE..........LQS.L.LM..G..VLTTN.D
Retrocopy KDQDLLVVAHDLIRKVSPRTGDTKPNFFQDCLMEVFDSLEQYIQNPA--VLQSILSLMDRGTMVLTTNYD

Parental  NLLELYAADQGKQLESLDLTDEKKVLEWAQEKRKLSV-LHIHGVYTNPSGIVLHPAGYQNVLRNTEVMRE
          NLLEL....Q.K..ESLDL.D..KVL.WA....K..V.LHIHG.YT.P.G.VL.P.GY..V....EVM..
Retrocopy NLLELFGQQQNKPMESLDLKDKTKVLQWARGHVKYGV<LHIHGLYTDPCGMVLDPSGYKDVTQDPEVMEV

Parental  IQKLYENKSFLFLGCGWTVDDTTFQALFLEAVKHKSDLEHFMLVRRGDVDEFKKLRENMLDKGIKVISYG
          .Q.LY..KSFLF.GCG.T..D..FQALFL..V..K.DLEH.MLV...D.D.F.K....ML..GIKV.SYG
Retrocopy LQNLYRTKSFLFVGCGETLRDQIFQALFLYSVPDKVDLEHYMLVLKEDEDHFFKHQADMLLHGIKVVSYG

Parental  NDYADLPEYFRRLTCEI
          ...A..P.Y...L...I
Retrocopy DCFAHFPGYVQDLATRI

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	10.49 RPM	8.66 RPM
SRP017611_kidney	3.65 RPM	10.54 RPM
SRP017611_liver	1.39 RPM	2.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1272 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1272 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016718	1 retrocopy	retro_dord_554,
Erinaceus europaeus	ENSEEUG00000007898	1 retrocopy	retro_eeur_605,
Myotis lucifugus	ENSMLUG00000017329	1 retrocopy	retro_mluc_1535,
Oryctolagus cuniculus	ENSOCUG00000017049	1 retrocopy	retro_ocun_1272 ,
Otolemur garnettii	ENSOGAG00000008923	1 retrocopy	retro_ogar_1659,