RetrogeneDB ID: retro_ocun_402

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:149533072..149533480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2T
• Ensembl ID: ENSOCUG00000010249
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2T (putative) [Source:HGNC Symbol;Acc:25009]

Sequence

>retro_ocun_402
AGAAGAACTTCATGCCTTAAGAGAGAGTTGCACATGTTAGCTACAGAGCCACCACCAGGCATTATGTGCTGGTAAGATAA
GGACTAAATGGATGATCTAGTATTCATAGCAATACTAGGTGGATCTAACACACCTTATGAGAAAGGTGTTTTCAAGCAGG
AAGTTATTATTCCTGAGAGGTACCTATTTAAATCTCCTAAATCTCCTCAGATCTGATTTCTGACTCCAATCTATCTGCCA
AACATTGATTCTGCTGGAAGAATTTGTCTAGATGTTTTCAAATTGCCACCAAAATGTGTCTGGAAACCATCCCTTAACAT
TGCAACTGTGTTGACCTCTATTCAGCTGCTCATGTCAGAACCCAACCCTGACGACCTGCTAATGGCTTATATTTCCTCAG
AATTTAAA

Alignment

ORF - retro_ocun_402 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 67.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRASRLKRELHMLATEPPPGITCWQEKDQMDDLR-AQILGGSNTPYEKGVFKLEVIIPERYPFEP---PQ
          .R.S.LKRELHMLATEPPPGI.CW..KD.MDDL....ILGGSNTPYEKGVFK.EVIIPERY.F.....PQ
Retrocopy RRTSCLKRELHMLATEPPPGIMCW*DKD*MDDLVFIAILGGSNTPYEKGVFKQEVIIPERYLFKSPKSPQ

Parental  IRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFK
          I.FLTPIY.PNIDSAGRICLDV.KLPPK..W.PSLNIATVLTSIQLLMSEPNPDD.LMA.ISSEFK
Retrocopy I*FLTPIYLPNIDSAGRICLDVFKLPPKCVWKPSLNIATVLTSIQLLMSEPNPDDLLMAYISSEFK

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	0.22 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.15 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_402 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_402 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_402 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000010249	3 retrocopies	retro_ocun_402 , retro_ocun_403, retro_ocun_910,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Otolemur garnettii	ENSOGAG00000029029	1 retrocopy	retro_ogar_1392,
Tarsius syrichta	ENSTSYG00000001704	4 retrocopies	retro_tsyr_1998, retro_tsyr_208, retro_tsyr_379, retro_tsyr_991,