RetrogeneDB ID: retro_ocun_669

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:120301715..120302205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP11L
• Ensembl ID: ENSOCUG00000007154
• Aliases: None
• Description: UTP11-like, U3 small nucleolar ribonucleoprotein, (yeast) [Source:HGNC Symbol;Acc:24329]

Sequence

>retro_ocun_669
AAGATTAAACTCCAGGATGGAGTTCATGTTATTAAGGAGACTAAGGACGATGTCGTTCCAGGACAGCTAAAGCTGATGAG
AACTCAGGATGTCAAATACAGAAGAATGAAAAAGATTGTAGAAGCCAAGAAAATCCAGTGACTAAATCAGAGCTCCATCT
GCTGGATTTCCAGGGGAGCAACAGAAGCAGCCTGTGCTCTTTTGCCACCAAAAAGGAAGCTGGACAGTTCGGTGTTGTGA
CTCGCCCGTAGACAATCCTGGAACCAGTTGGCAGAGTCTTCAATAGACCCAGGTAGAGACCTTGCAGAAGGAAAAAGTGA
AAGCAGTTACCCATCACACTCGCCGCAAGCGGATAGCTAGAGAGAGGCAGGAGCAACACAGCTGCCTGACTCAGCAGACT
GAATGAGAGGAGAACCTGTTCCATATTGCACAGGAAATTCAAACTTGCCAAGATCTCATGCATACAACTCACAAGGCAAA
GGCGAAGAAA

Alignment

ORF - retro_ocun_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.07 %
• Parental protein coverage: 71.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVKLQDGVHVIKETKEEVTPEQLKLMRTQDVKYIEMKRVAEAKKIERL-KSELHLLDFQGKQQNKHVFFF
          ..KLQDGVHVIKETK..V.P.QLKLMRTQDVKY..MK...EAKKI..L.KSELHLLDFQG.........F
Retrocopy KIKLQDGVHVIKETKDDVVPGQLKLMRTQDVKYRRMKKIVEAKKIQ*L<KSELHLLDFQGSNRSS-LCSF

Parental  DTKKEVEQFDVATHLQTAPELVDRVFNRPR-IETLQKEKVKGVTHQTRLKRIAKERQKQYNCLIQRIERE
          .TKKE..QF.V.T...T..E.V.RVFNRPR..ETLQKEKVK.VTH.TR.KRIA.ERQ.Q..CL.Q..E.E
Retrocopy ATKKEAGQFGVVTRP*TILEPVGRVFNRPR<VETLQKEKVKAVTHHTRRKRIARERQEQHSCLTQQTE*E

Parental  KELFVTAQKIQTRKDLMDKTQKVKVKK
          ..LF..AQ.IQT..DLM..T.K.K.KK
Retrocopy ENLFHIAQEIQTCQDLMHTTHKAKAKK

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	3.81 RPM	12.03 RPM
SRP017611_kidney	1.11 RPM	20.37 RPM
SRP017611_liver	0.00 RPM	5.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_669 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001043	1 retrocopy	retro_cpor_1084,
Microcebus murinus	ENSMICG00000001496	1 retrocopy	retro_mmur_894,
Myotis lucifugus	ENSMLUG00000001003	1 retrocopy	retro_mluc_2386,
Mus musculus	ENSMUSG00000028907	1 retrocopy	retro_mmus_1968,
Oryctolagus cuniculus	ENSOCUG00000007154	2 retrocopies	retro_ocun_1285, retro_ocun_669 ,
Otolemur garnettii	ENSOGAG00000016492	2 retrocopies	retro_ogar_3229, retro_ogar_3324,
Rattus norvegicus	ENSRNOG00000007174	1 retrocopy	retro_rnor_1838,