RetrogeneDB ID: retro_vpac_73

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_1543:563536..564121(-)
• Located in intron of: ENSVPAG00000005180

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTP1
• Ensembl ID: ENSVPAG00000008003
• Aliases: None
• Description: glutathione S-transferase pi 1 [Source:HGNC Symbol;Acc:4638]

Sequence

>retro_vpac_73
CGCTGCGAGGCCATGCACATGCTGCTGGCTGACCAGGACCAGAGCTGGAAGGAGGAGGTGGAGACCATGGAGACCTGGCC
TGCACTCAAACCCTCCTGTCTGTACGGGCAGCTCCCCAAGTTCCAGGATGGAGATCTCACCCTGTACCAGTCCAATGCCA
TTCTGCGTCACCTGGGCCGCTCACTTGGACTGTATGGGAAGGACCAGCAGGAGGCAGCCCTTTTGGACGTGGTGAATGAT
GGCGTGGAGGACCTCCGTTGCAAATATGCCACCCTCATCTACACCAACTACGAGGCAGGCAAGGAGGGCTATGTGAAGGC
ACTGCCGGAGCATCTGAAGCCTTTTGAGACCCTGCTGTCCCAGAACCAGGGAGGCCAGGCCTTCATCGTGGGCAACCAGA
TCTCCTTCGCAGACTACAACCTGCTGGACTTGCTGCTGAATCACCAGGTCCTGGCCCCTGGCTGCCTGGACTCCTTCCCC
CTGCTCTCAGCCTACGTGGCTCGCCTCAGTGCCCGGCCCAAGCTCAAGGCCTTCTTGGCCTCCCCTGAGCACGTGAAGCG
CCCTATCAATGGCAACGGGAAGCAG

Alignment

ORF - retro_vpac_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  RCEAMHMLLADQDQSWKEEVETMETWPALKPSCLYGQLPKFQDGDLTLYQSNAILRHLGRSLGLYGKDQQ
          RCEAMHMLLADQDQSWKEEVETMETWPALKPSCLYGQLPKFQDGDLTLYQSNAILRHLGRSLGLYGKDQQ
Retrocopy RCEAMHMLLADQDQSWKEEVETMETWPALKPSCLYGQLPKFQDGDLTLYQSNAILRHLGRSLGLYGKDQQ

Parental  EAALLDVVNDGVEDLRCKYATLIYTNYEAGKEGYVKALPEHLKPFETLLSQNQGGQAFIVGNQISFADYN
          EAALLDVVNDGVEDLRCKYATLIYTNYEAGKEGYVKALPEHLKPFETLLSQNQGGQAFIVGNQISFADYN
Retrocopy EAALLDVVNDGVEDLRCKYATLIYTNYEAGKEGYVKALPEHLKPFETLLSQNQGGQAFIVGNQISFADYN

Parental  LLDLLLNHQVLAPGCLDSFPLLSAYVARLSARPKLKAFLASPEHVKRPINGNGKQ
          LLDLLLNHQVLAPGCLDSFPLLSAYVARLSARPKLKAFLASPEHVKRPINGNGKQ
Retrocopy LLDLLLNHQVLAPGCLDSFPLLSAYVARLSARPKLKAFLASPEHVKRPINGNGKQ

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_73 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_73 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001020	3 retrocopies	retro_amel_1921, retro_amel_249, retro_amel_778,
Canis familiaris	ENSCAFG00000011349	4 retrocopies	retro_cfam_143, retro_cfam_2043, retro_cfam_46, retro_cfam_617,
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Macropus eugenii	ENSMEUG00000001519	2 retrocopies	retro_meug_1519, retro_meug_1762,
Mustela putorius furo	ENSMPUG00000004029	2 retrocopies	retro_mputfur_1215, retro_mputfur_1463,
Mus musculus	ENSMUSG00000038155	1 retrocopy	retro_mmus_521,
Oryctolagus cuniculus	ENSOCUG00000002230	1 retrocopy	retro_ocun_391,
Rattus norvegicus	ENSRNOG00000018237	4 retrocopies	retro_rnor_2140, retro_rnor_2567, retro_rnor_2842, retro_rnor_769,
Tursiops truncatus	ENSTTRG00000003746	1 retrocopy	retro_ttru_1416,
Vicugna pacos	ENSVPAG00000008003	1 retrocopy	retro_vpac_73 ,