RetrogeneDB ID: retro_rnor_799

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:44923139..44923856(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vta1
• Ensembl ID: ENSRNOG00000011540
• Aliases: Vta1, Lip5, RGD1305031
• Description: vacuolar protein sorting-associated protein VTA1 homolog [Source:RefSeq peptide;Acc:NP_001020811]

Sequence

>retro_rnor_799
ACTCTTAAGAAACAGTTAGGGAATAATGAAACTGTTACTCAAGAAATAGTTGGTTGTGCCCATTTGGAAAATTATGCTTT
GAAAATGTTCTGGTACATAGACAACGAAGACTGAGCTGGACGATTTCACAAAAACATGATCAAGTCCTTCTACACTGCTC
ACCTTTTAATAGATGTCATCACAGTATTTGGTGAAATCACAGATGAAAATGTGAAACATAGAAAGTACGCCAGGTGGAAG
GCAACATATATTCATAACTGCTTAAAGAGTTGGGAGACTCCTCAAGCAGGGCCTGTTGGAATCGAGGAAAATAACGATGT
TAAAGAAAATGAAGATGTTGGTGCAACCTCTCTGCCTACTCAGCCACCACAGCCGTCATCATCTTCAACATACGACCCAA
GCAACTTGGCAACAGGCAGCTACAGTGGGATGCAGATTTCTCCAGGTGCACCAGCCAATACTCCTGCAAAAGTGCCACAC
AGCACAGGTACAACAAGTAATGCCTTCCAGCCTAGTCCACAGTCTGTCCCAGCCATTCCAGCCACTGATCCTGACCTGTA
CACAGCTTCCCAAGGGGATATCCGCCTGACCCCAGAGGACTTTGCTCGAGCTCAGACGTACTGTAAGTGCGCTGGGAATG
CACTACTGTATGAAGGTGTGGGCACCGCTGTGCAGAACCTACAGAAGGCTCTCAGGCTGCTGACAACAGGCAAGGAG

Alignment

ORF - retro_rnor_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.97 %
• Parental protein coverage: 96.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLKKQLGDNEAVTQEIVGCAHLENYALKMFLYADNEDRAGRFHKNMIKSFYTASLLIDVITVFGELTDEN
          TLKKQLG.NE.VTQEIVGCAHLENYALKMF.Y.DNED.AGRFHKNMIKSFYTA.LLIDVITVFGE.TDEN
Retrocopy TLKKQLGNNETVTQEIVGCAHLENYALKMFWYIDNED*AGRFHKNMIKSFYTAHLLIDVITVFGEITDEN

Parental  VKHRKYARWKATYIHNCLKNGETPQAGPVGIEEDNDVEENEDVGATSLPTQPPQPSSSSTYDPSNLAAGS
          VKHRKYARWKATYIHNCLK..ETPQAGPVGIEE.NDV.ENEDVGATSLPTQPPQPSSSSTYDPSNLA.GS
Retrocopy VKHRKYARWKATYIHNCLKSWETPQAGPVGIEENNDVKENEDVGATSLPTQPPQPSSSSTYDPSNLATGS

Parental  YSGIQIPPGAHAPANTPAEVPHSTGVTSNAVQPSPQTVPAIPAIDPDLYTASQGDVRLTPEDFARAQKYC
          YSG.QI.PG..APANTPA.VPHSTG.TSNA.QPSPQ.VPAIPA.DPDLYTASQGD.RLTPEDFARAQ.YC
Retrocopy YSGMQISPG--APANTPAKVPHSTGTTSNAFQPSPQSVPAIPATDPDLYTASQGDIRLTPEDFARAQTYC

Parental  KYAGSALQYEDVSTAVQNLQKALRLLTTGRE
          K.AG.AL.YE.V.TAVQNLQKALRLLTTG.E
Retrocopy KCAGNALLYEGVGTAVQNLQKALRLLTTGKE

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	36.31 RPM
SRP017611_kidney	0.00 RPM	32.73 RPM
SRP017611_liver	0.00 RPM	11.16 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_799 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_799 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,