RetrogeneDB ID: retro_vpac_621

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_7905:10252..10738(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000011775
• Aliases: None
• Description: None

Sequence

>retro_vpac_621
ATGGCGTCGGGGCCGGGCGGGTGGCTTGGACCGGCGTTCGCACTGCGCCTGCTGCTGGCCACCGTGCTTCAAGAGGTGTC
CACGTTCAGGGCAGAGTTTTCATCAGAGTCTTGCAGGGAGTTAGGCTTCTCCAGCAACTTGCTCTGCAGTTCCTGTGATC
TTCTCGGACAGTTCAACCTTCTTCAGCTGGATCCTGACTGTAGAGGATGCTGTCAGGAAGAAGCACAATTTGAAACCAAA
AAGCTGTATGCAGGAGCTATTCTTGAAGTCTGTGGATGAAAACTGGGGAGGTTCCCTCAAGTCCAAGCTTTTGTCAGGAG
TGATAAACCCAAACTATTCAGAGGACTACAAATCAAGTATGTTCGTGGTTCAGACCCTGTGCTGAAGCTTTTGGACGACA
ATGGGAACATTGCTGAGGAGCTCAGCATCCTCAAATGGAACACAGGCAGTGTAGAAGAATTTCTGAGTGAAAAGTTGGAG
CGTATA

Alignment

ORF - retro_vpac_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.15 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGPGGWLGPAFALRLLLATVLQEVSAFRAEFSSESCRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGC
          MASGPGGWLGPAFALRLLLATVLQEVS.FRAEFSSESCRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGC
Retrocopy MASGPGGWLGPAFALRLLLATVLQEVSTFRAEFSSESCRELGFSSNLLCSSCDLLGQFNLLQLDPDCRGC

Parental  CQEEAQFETKKLYAGAILEVCGUKLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEE
          CQEEAQFETKKLYAGAILEVCG.KLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEE
Retrocopy CQEEAQFETKKLYAGAILEVCG*KLGRFPQVQAFVRSDKPKLFRGLQIKYVRGSDPVLKLLDDNGNIAEE

Parental  LSILKWNTDSVEEFLSEKLERI
          LSILKWNT.SVEEFLSEKLERI
Retrocopy LSILKWNTGSVEEFLSEKLERI

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_621 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_621 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004701	1 retrocopy	retro_dnov_2296,
Macropus eugenii	ENSMEUG00000005462	4 retrocopies	retro_meug_1005, retro_meug_2191, retro_meug_769, retro_meug_817,
Monodelphis domestica	ENSMODG00000008134	2 retrocopies	retro_mdom_1289, retro_mdom_1504,
Ochotona princeps	ENSOPRG00000003411	2 retrocopies	retro_opri_157, retro_opri_897,
Vicugna pacos	ENSVPAG00000011775	1 retrocopy	retro_vpac_621 ,