RetrogeneDB ID: retro_ocun_1894

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:64025756..64026170(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000020968
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DCTN3
• Ensembl ID: ENSOCUG00000000358
• Aliases: None
• Description: dynactin 3 (p22) [Source:HGNC Symbol;Acc:2713]

Sequence

>retro_ocun_1894
GGGTTGGGTTGGGCACATAAGGTAGCTTACGGCCTGGTCAAGGTGAAGGTGGCTTTGGGGGACATACCTAACAGGCAAAA
GAAGGTGAAGATTCTGTACAAACAAGTTGAAGACCTGATCAATACCTGGATCCTGAGGACATCAACTGCAGGGCCATTAT
CTGATGCCTTTGAGCTGCAGTTCATCTTAACAGAGGAGCAGCTTCTCTTCTCCCTGGCTGCACAACTGGCGCAGGTAGAC
GCCTTGGCTCCCATACTGGACAGTGCTCAGTTCAAAGCCGTTCCTGAGCATGACACCTGCCTGTGGCTCTTGGCCCAGAT
CCACATCCGCCAGCAGGATCAGTGGATGCAGATCCCAGAGGAGTCCAAAGCTCTCCTGGAGAACTACAAGACTACGATGC
TGCTCTCCAAGCAA

Alignment

ORF - retro_ocun_1894 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.54 %
• Parental protein coverage: 74.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVRGSRKVADGLVKVQVALGNIASKRERVKILYKKIEDLI-KYLDPEYIDRIAI-PDASKLQFILAEEQF
          G.....KVA.GLVKV.VALG.I......VKILYK..EDLI..YLDPE.I...AI..DA..LQFIL.EEQ.
Retrocopy GLGWAHKVAYGLVKVKVALGDIPNRQKKVKILYKQVEDLI<QYLDPEDINCRAI>SDAFELQFILTEEQL

Parental  ILAQVALLEQVDALVPMLDSAHIKAVPEHAARLQRLAQIHIQQQDQCMEITEESKALLEEYNKTTMLLSK
          .....A.L.QVDAL.P.LDSA..KAVPEH...L..LAQIHI.QQDQ.M.I.EESKALLE.Y.KTTMLLSK
Retrocopy LFSLAAQLAQVDALAPILDSAQFKAVPEHDTCLWLLAQIHIRQQDQWMQIPEESKALLENY-KTTMLLSK

Parental  Q
          Q
Retrocopy Q

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	44.21 RPM
SRP017611_kidney	0.00 RPM	42.57 RPM
SRP017611_liver	0.00 RPM	7.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1894 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1894 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1894 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
Oryctolagus cuniculus	ENSOCUG00000000358	1 retrocopy	retro_ocun_1894 ,
Rattus norvegicus	ENSRNOG00000014208	1 retrocopy	retro_rnor_562,