RetrogeneDB ID: retro_ocun_1568

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:8052199..8052585(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC12
• Ensembl ID: ENSOCUG00000008694
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 12 [Source:HGNC Symbol;Acc:28908]

Sequence

>retro_ocun_1568
AAGAGTCAAGCCTGTTATGACCACTGGAGAAGGAGTCAGATGCTGAAGCCATTTCTACATGGGAAGCTTTGACTGACTCA
GTGAAAACATCAATGCAGTGGGCTGCTAGAGGTAAAAAGAATCTGATGTTGGAGGAAGCTGATCAGACTCACACAAACAA
GATTGAAAATGAGAACTGGAATGAACAAAGAGAAATAACAGAAGATGAAATGGTTCCAATCACAGAAAAAATTAAGCAAA
ATGAGTCTGAGTCCCTAGAGAAGTCAAGCTCACAGCAAAATCCAGATTCTCAAAGTTTTTCCAGCATGAACTGTTGGCAC
TTTCGTTTCCACTGGCCCAGGTATGCTCCTTCAGAACTCCTGAGAAAGTTCAGATACTATAAAATA

Alignment

ORF - retro_ocun_1568 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 65.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESRARYDHWRRSQMSIPF-QQWEALTDSVKTSMHWAVRGKKDLMLEESDQTHTNKIGNEDWDKQREIKEE
          .S.A.YDHWRRSQM..PF...WEALTDSVKTSM.WA.RGKK.LMLEE.DQTHTNKI.NE.W..QREI.E.
Retrocopy KSQACYDHWRRSQMLKPF<STWEALTDSVKTSMQWAARGKKNLMLEEADQTHTNKIENENWNEQREITED

Parental  EMGPTTEKMKKKECESLEKSSSQQNPDSPSFSDVNCWHLRFRWSGGAPSELLRKFRNYEI
          EM.P.TEK.K..E.ESLEKSSSQQNPDS.SFS..NCWH.RF.W...APSELLRKFR.Y.I
Retrocopy EMVPITEKIKQNESESLEKSSSQQNPDSQSFSSMNCWHFRFHWPRYAPSELLRKFRYYKI

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	66.56 RPM
SRP017611_kidney	0.00 RPM	77.84 RPM
SRP017611_liver	0.00 RPM	14.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1568 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1568 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1568 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009276	1 retrocopy	retro_lafr_855,
Oryctolagus cuniculus	ENSOCUG00000008694	1 retrocopy	retro_ocun_1568 ,