RetrogeneDB ID: retro_vpac_397

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_156697:146..362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM3
• Ensembl ID: ENSVPAG00000010709
• Aliases: None
• Description: LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17874]

Sequence

>retro_vpac_397
ATGAAAACGGGAAATGACAGAGAGCTTCAAGGCAGGTTACATGCTTACGATCAACATTTAAATATGACATTGGGAGATGA
GGAAGGAACTGTGACAACTATAGAAACTGATGAAGAAACATATGAAGAGATACATAAATCAGCAAAAGGGAATATTCTGA
TGCTCTTGGTCTGGGGAGATGGGGTTGTGCTAGTTGACCCGTCATTGAGAGGTGGA

Alignment

ORF - retro_vpac_397 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.39 %
• Parental protein coverage: 75.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEETYEEIYKSTKRNIPMLFVRGDGVVLVAPPLR
          .K..NDREL.GRLHAYDQHLNM.LGD.E.TVTTIE.DEETYEEI.KS.K.NI.ML.V.GDGVVLV.P.LR
Retrocopy MKTGNDRELQGRLHAYDQHLNMTLGDEEGTVTTIETDEETYEEIHKSAKGNILMLLVWGDGVVLVDPSLR

Parental  VG
          .G
Retrocopy GG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_397 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_397 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016977	1 retrocopy	retro_cjac_54,
Gorilla gorilla	ENSGGOG00000010006	4 retrocopies	retro_ggor_104, retro_ggor_1699, retro_ggor_2068, retro_ggor_826,
Myotis lucifugus	ENSMLUG00000010677	4 retrocopies	retro_mluc_1148, retro_mluc_2306, retro_mluc_2337, retro_mluc_25,
Monodelphis domestica	ENSMODG00000007275	1 retrocopy	retro_mdom_800,
Oryctolagus cuniculus	ENSOCUG00000011088	1 retrocopy	retro_ocun_126,
Otolemur garnettii	ENSOGAG00000007659	6 retrocopies	retro_ogar_1031, retro_ogar_231, retro_ogar_242, retro_ogar_2490, retro_ogar_2818, retro_ogar_577,
Oreochromis niloticus	ENSONIG00000000370	1 retrocopy	retro_onil_12,
Sus scrofa	ENSSSCG00000011601	6 retrocopies	retro_sscr_1134, retro_sscr_1140, retro_sscr_395, retro_sscr_396, retro_sscr_457, retro_sscr_64,
Vicugna pacos	ENSVPAG00000010709	2 retrocopies	retro_vpac_121, retro_vpac_397 ,