RetrogeneDB ID: retro_vpac_23

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_3235:96287..96932(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSVPAG00000004626
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000000700
• Aliases: None
• Description: None

Sequence

>retro_vpac_23
AGAACAATGGCTCAGGAGACTAACCAGACCCCAGGGCCCATGCTGTGTAGTACAGGATGTGGCTTTTATGGGAATCCTAG
GACAAATGGAATGTGTTCTGTTTGCTTCAAAGAACATCTTCAGAGACAGCAGAAGAGTGGCAGAATGAGCCCAATGGGAA
CAGCTAGTGGTTCCAACAGTCCTACCTCAGATTCTGCATCTGTACAAAGGGCAGATACTAGTTTAAACAACTGTGAAGGT
GCTGCTGTCAGCACAACTGAAAAATCAAGAAATGTGCCTGTGGCTGCCTTGCCTGTAACGCAGCAAATGACAGAAATGAG
CATTTCAAGAGAAGACAAAATAACTACCCCGAAAACAGAGGTGTCAGAGCCAGTTGTCACTCAGCCCAGTCCATCAGTTT
CTCAGCCCAGTACTTCTCAAAGTGAAGAAAAATCTCCTGAGTTGCCCAAACCAAAGAACAGATGTTTCATGTGCAGAAAG
AAAGTTGGCCTTACAGGGTTTGACTGCCAATGTGGAAATTTGTTTTGTGGACTTCACCGTTACTCTGACAAGCACAACTG
TCCTTATGATTACAAAGCAGAAGCTGCAGCAAAAAGCAGAAAAGAGAATCCAGTTGTTGTGGCTGAAAAAATCCAGAGAA
TATAA

Alignment

ORF - retro_vpac_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.7 %
• Parental protein coverage: 98.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCYKEHLQRQQNSGRMSPMGTASGSNSPTSDSASVQRADT
          AQETNQTPGPMLCSTGCGFYGNPRTNGMCSVC.KEHLQRQQ.SGRMSPMGTASGSNSPTSDSASVQRADT
Retrocopy AQETNQTPGPMLCSTGCGFYGNPRTNGMCSVCFKEHLQRQQKSGRMSPMGTASGSNSPTSDSASVQRADT

Parental  SLNNCEGAAGSTTEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPSTSQSEE
          SLNNCEGAA.STTEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPSTSQSEE
Retrocopy SLNNCEGAAVSTTEKSRNVPVAALPVTQQMTEMSISREDKITTPKTEVSEPVVTQPSPSVSQPSTSQSEE

Parental  KAPELPKPKKNRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKAEAAAKIRKENPVVVAEKIQ
          K.PELPKP.KNRCFMCRKKVGLTGFDC.CGNLFCGLHRYSDKHNCPYDYKAEAAAK.RKENPVVVAEKIQ
Retrocopy KSPELPKP-KNRCFMCRKKVGLTGFDCQCGNLFCGLHRYSDKHNCPYDYKAEAAAKSRKENPVVVAEKIQ

Parental  RI
          RI
Retrocopy RI

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_23 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_23 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23 ,