RetrogeneDB ID: retro_ocun_1864

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019558:4056..4757(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTA1
• Ensembl ID: ENSOCUG00000002554
• Aliases: None
• Description: Vps20-associated 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:20954]

Sequence

>retro_ocun_1864
GGTGATAATGAAGCTATTACCCAAGGAGTAGTTGGTTCTGCCCATTTGAGGAATTATTCTTGGATAATGTTTATATATGC
AGACAGTGAACATTGTGCTGGGTAATTTCACAAAAAAACATGATCAAGTTCTTCTATACTGCAAGTCTTTTAATAGATGT
CATAACTGTGTTTGACATAACACTGATGAAAATGTGAAACACACAAAGTATGCAAGGTGGAAGGCAACATATATCCATAA
TTGCTTAAACAATGAGGAGACTCCTCAAGCAGGCCCTATTGCAATTGAGGAAGATACTGATGGTGAAGAAAATGAAGATG
CTGTAGTAGCATCTCTGCCCACTCAACACACCTCAGCCATCATCATCTTCAGCAGTTGACCCAGGCAGCATGCCATCAGA
CAGCTATAGTTGAATACAGATTCCTCTGGGTGCACATGCCACAGCCAACACACCAGCGAAAGTGCCTCATAGCATGGGTG
TAACAAGGAATACCATCCAACCTACTCTATAGACTATGCCAGCCATTGATCCTGCACTTTCCAGTACGGTTTCCCAAGGC
GATACCCACCTCACCCCTGAGGACTTTGTGAGAGCTCAGAGATACTGCAAATATGCTCACAGTGCTTTTCAATATGAAGA
TGTAAGCACTGCCATTCAGAATCTACAGAAAGCCCTCAAGCTACTGATGACTGACAGAGAA

Alignment

ORF - retro_ocun_1864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.48 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GDNEAITQEIVGSAHLENYALKMFLYADNEDRA-GRF-HKNMIKSFYTASLLIDVITVFG-ELTDENVKH
          GDNEAITQ..VGSAHL.NY...MF.YAD.E..A.G.F..KNMIK.FYTASLLIDVITVF....TDENVKH
Retrocopy GDNEAITQGVVGSAHLRNYSWIMFIYADSEHCA>GNF>QKNMIKFFYTASLLIDVITVFD<HNTDENVKH

Parental  RKYARWKATYIHNCLKNGETPQAGPVGIEEDNDGEENEDAGVASLPTQ-PPQPSSSSAFDPGSMPSGSYS
          .KYARWKATYIHNCL.N.ETPQAGP..IEED.DGEENEDA.VASLPTQ..PQPSSSSA.DPGSMPS.SYS
Retrocopy TKYARWKATYIHNCLNNEETPQAGPIAIEEDTDGEENEDAVVASLPTQ>TPQPSSSSAVDPGSMPSDSYS

Parental  GIQIPPGAHAPANTPAEVPHGTGVTSNTIQPAPQTIPAIDPALFSTVSQGDIRLTPEDFARAQKYCKYAG
          .IQIP.GAHA.ANTPA.VPH..GVT.NTIQP...T.PAIDPAL.STVSQGD..LTPEDF.RAQ.YCKYA.
Retrocopy *IQIPLGAHATANTPAKVPHSMGVTRNTIQPTL*TMPAIDPALSSTVSQGDTHLTPEDFVRAQRYCKYAH

Parental  SALQYEDVSTAVQNLQKALKLLTTGRE
          SA.QYEDVSTA.QNLQKALKLL.T.RE
Retrocopy SAFQYEDVSTAIQNLQKALKLLMTDRE

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	16.39 RPM
SRP017611_kidney	0.00 RPM	12.26 RPM
SRP017611_liver	0.00 RPM	4.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1864 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1864 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1864 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000009844	1 retrocopy	retro_hsap_4088,
Gorilla gorilla	ENSGGOG00000015524	1 retrocopy	retro_ggor_2742,
Microcebus murinus	ENSMICG00000004420	2 retrocopies	retro_mmur_1290, retro_mmur_290,
Macaca mulatta	ENSMMUG00000023012	1 retrocopy	retro_mmul_751,
Nomascus leucogenys	ENSNLEG00000015053	1 retrocopy	retro_nleu_1911,
Oryctolagus cuniculus	ENSOCUG00000002554	10 retrocopies	retro_ocun_1543, retro_ocun_1689, retro_ocun_1790, retro_ocun_1810, retro_ocun_1821, retro_ocun_1832, retro_ocun_1848, retro_ocun_1853, retro_ocun_1864 , retro_ocun_965,
Pan troglodytes	ENSPTRG00000018662	1 retrocopy	retro_ptro_2773,
Rattus norvegicus	ENSRNOG00000011540	1 retrocopy	retro_rnor_799,
Tursiops truncatus	ENSTTRG00000014998	1 retrocopy	retro_ttru_1825,