RetrogeneDB ID: retro_ocun_1651

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018741:1972692..1973218(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC115
• Ensembl ID: ENSOCUG00000005099
• Aliases: None
• Description: coiled-coil domain containing 115 [Source:HGNC Symbol;Acc:28178]

Sequence

>retro_ocun_1651
GTGGTGGCCCGGGACGTGCAGGCGGAACTGGATTCGCTGATCCTGCAGCTGCTCGCGGACCTGGAGGAGCTGGAGGCGAA
ACGGGAGGCGCTGCACGGCCCTGTGGAGGAGGGCTGGATGTCGCTCGTCCAGGCGCGCTAGGCCATGGGTGAGAAGTAGG
TAGGCCCCCTGCAGTACGCCTAACACACGGAGCCCCAGGTGTGTATGTGAGCCAGCGGGGCCCCGGAGGGACCCAGAACT
TGCTAGTGGTGAGAGCCGGCGCCCAGATCCCGGAGAAGGTGGGGCCCCTTGAGGCAGCTCTGCGCCAGCGCCAGGGCCCC
ACCAAGACGCCGGAGCCCGAGCCCCAGCGCCCCAGGACCCCCTGAACTGGTTCGGAATCCTGGTTTTTCAGTCTGCTGCG
GGCGCAAGCCAGCTTCAGGGATGGCCTGCAGCTAGCTGGGGACATTGCCCCCCTCCAGATCCGCTTAGCTGGGGTCAGAG
GCAGCTCCGGAAGCTCCAGGAGAAACTCAGGCAGCTTGAACCGGGC

Alignment

ORF - retro_ocun_1651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.47 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAARDVRTELDSLILQLLADLEELEAKRAALNGRVEEGWLSLAQARYAMGVKSVGPLQYASRMEPQVCVC
          ..ARDV..ELDSLILQLLADLEELEAKR.AL.G.VEEGW.SL.QAR.AMG.K.VGPLQYA...EPQVC..
Retrocopy VVARDVQAELDSLILQLLADLEELEAKREALHGPVEEGWMSLVQAR*AMGEK*VGPLQYA*HTEPQVCM*

Parental  ASEAPD-GLQNLRVVRAGAQIPEEVGPREAALRRRKGPTKTPEPESTTAPQDP-LNWFGILVPHS-LRQA
          AS.AP..G.QNL.VVRAGAQIPE.VGP.EAALR.R.GPTKTPEPE....P..P.LNWFGILV..S.LR.A
Retrocopy ASGAPE<GTQNLLVVRAGAQIPEKVGPLEAALRQRQGPTKTPEPE-PQRPRTP<LNWFGILVFQS>LR-A

Parental  QASFRDGLQLAGDIATLQIR-ISWGQSQLRKLQEKLRQLEPG
          QASFRDGLQLAGDIA.LQIR..SWGQ.QLRKLQEKLRQLEPG
Retrocopy QASFRDGLQLAGDIAPLQIR<LSWGQRQLRKLQEKLRQLEPG

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	7.34 RPM
SRP017611_kidney	0.00 RPM	9.63 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1651 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1651 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000010588	2 retrocopies	retro_mdom_200, retro_mdom_435,
Mus musculus	ENSMUSG00000042111	2 retrocopies	retro_mmus_2696, retro_mmus_380,
Oryctolagus cuniculus	ENSOCUG00000005099	1 retrocopy	retro_ocun_1651 ,
Otolemur garnettii	ENSOGAG00000000166	2 retrocopies	retro_ogar_2849, retro_ogar_3466,
Tursiops truncatus	ENSTTRG00000012598	1 retrocopy	retro_ttru_781,