RetrogeneDB ID: retro_ocun_1285

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:2567164..2567509(+)
• 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_1285
TTTCAAGAACATCTGGGCTTGCTAGAGAAAAAGAAAGATTACAAACTGCACTAATGACTGCCATAAAAACAAGAATACCT
CAGAGCTCTCTGGAAGAAGATGCTTAAAAAACATCCAGATGAATTTTACTATAAAATGATTCATGTTAGACTCCAGGATG
GAATTCATCTTATTAAGGAGACAAAGGAAGATGTAACTCTAGAACAGATAAAGCTGATGAGAACTCAGGCTGTCAAATAT
ATAGAAATGAAAAGGGATGCAGAAGCTAAGAAAATTGAAAGACTAAAATCAGAGCTCCATCTGCTGGATTTCCAGGGGAA
GCAACAGAATAAGCATGTGTTTTTT

Alignment

ORF - retro_ocun_1285 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.47 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FRKHLGLLE-KKKRYRPRF-SDYHK-KQEYLRALRKKALEKNPDEFYYKMTRVKLQDGVHVIKETKEEVT
          F..HLGLLE..K.R.......D.HK.KQEYLRAL.KK.L.K.PDEFYYKM..V.LQDG.H.IKETKE.VT
Retrocopy FQEHLGLLE<EKERLQTAL<NDCHK<KQEYLRALWKKMLKKHPDEFYYKMIHVRLQDGIHLIKETKEDVT

Parental  PEQLKLMRTQDVKYIEMKRVAEAKKIERLKSELHLLDFQGKQQNKHVFF
          .EQ.KLMRTQ.VKYIEMKR.AEAKKIERLKSELHLLDFQGKQQNKHVFF
Retrocopy LEQIKLMRTQAVKYIEMKRDAEAKKIERLKSELHLLDFQGKQQNKHVFF

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	0.28 RPM	12.03 RPM
SRP017611_kidney	0.10 RPM	20.37 RPM
SRP017611_liver	0.08 RPM	5.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1285 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1285 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1285 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,