RetrogeneDB ID: retro_vpac_566

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_4718:82659..83100(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEAF6
• Ensembl ID: ENSVPAG00000001916
• Aliases: None
• Description: MYST/Esa1-associated factor 6 [Source:HGNC Symbol;Acc:25674]

Sequence

>retro_vpac_566
GAAACACTGGCAAATTTGGAGAGACAGATCTATGCTTTTGAAGGAAGCTACCTGGAAGACACTCAGATGTATGGCAATAT
TATTCGTGGCTGGGATCGGTATCTGACCAACCAAAAAAACTCCAACAGCAAGAACGATCGGAGAAACCGGAAGTTCAAGG
AAGCGGAGCGGCTCTTCAGTAAATCCTCAGTGACTTCAGCAGCTGCAGTAAGTGCATTGGCAGGAGTTCAGGACCAGCTC
ATTGAAAAGAGAGAGCCAGGAAGTGGGACGGAAAGTGATACTTCTCCAGACTTCCACAATCAGGAAAATGAGCCCAGCCA
GGAGGACCCCGAGGATCTGGATGGATCTGTGCAGGGAGTGAAACCTCAGAAGGCTGCTGCTTCTACTTCCTCAGGGAGTC
ATCACAGCAGCCACAAAAAACGAAAGAATAAAAACCGGCAC

Alignment

ORF - retro_vpac_566 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.32 %
• Parental protein coverage: 85.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETLANLERQIYAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNSKNDRRNRKFKEAERLFSKSSVTSAAAV
          ETLANLERQIYAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNSKNDRRNRKFKEAERLFSKSSVTSAAAV
Retrocopy ETLANLERQIYAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNSKNDRRNRKFKEAERLFSKSSVTSAAAV

Parental  SALAGVQDQLIEKREPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQKAASSTSSGSHHSSHKK
          SALAGVQDQLIEKREPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQKAA.STSSGSHHSSHKK
Retrocopy SALAGVQDQLIEKREPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQKAAASTSSGSHHSSHKK

Parental  RKNKNRH
          RKNKNRH
Retrocopy RKNKNRH

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_566 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_566 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001927	1 retrocopy	retro_cjac_2767,
Cavia porcellus	ENSCPOG00000025988	1 retrocopy	retro_cpor_1252,
Erinaceus europaeus	ENSEEUG00000013971	3 retrocopies	retro_eeur_362, retro_eeur_469, retro_eeur_654,
Macropus eugenii	ENSMEUG00000003403	3 retrocopies	retro_meug_1279, retro_meug_584, retro_meug_727,
Myotis lucifugus	ENSMLUG00000017128	2 retrocopies	retro_mluc_436, retro_mluc_960,
Otolemur garnettii	ENSOGAG00000006773	1 retrocopy	retro_ogar_2339,
Vicugna pacos	ENSVPAG00000001916	1 retrocopy	retro_vpac_566 ,