RetrogeneDB ID: retro_vpac_17

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3714:615665..616073(-)
• Located in intron of: ENSVPAG00000011741

Retrocopy information

• Ensembl ID: ENSVPAG00000011743
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSVPAG00000002594
• Aliases: None
• Description: None

Sequence

>retro_vpac_17
ATGGCTACCCTCAGACCCCTCATGAAGCCCAAGATCGCCAAAAAGAGGACCAAAAAGTTCATCTGGCACCAGTCAGACCG
ATATGTCAAAATTAAGCGGAACTGGTGGAAACCCAGAGGCATTGACAGCAGGGTGTGCAGGAGGTTCAAGGGCCAGATCC
TGATGCCCAGCATCGGCTACGGGAGCAACAAGAAAACAAAGCACATGCTACCCAGCGGCTTCCGCAAGTTCCTGGTCCAC
AATGTCAAGGAGCTTGAAGTGCTGCTGATGTGCAACAAATCTTACTGTGCTGAGATTGCTCACAACTTCTCCTCCAAGAA
CTGCAAAGCTGTTGTGGAAAGAGCAGCCCAGCTGGCCATCAGAGTCACCAATCCCAACGCCAGGCTGCTCAGTGAAGAAG
ACAAATAG

Alignment

ORF - retro_vpac_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKXXXXXXXXXXNRVRRRCKGQI-MPSIGYGSNKKTKHML
          MA.LRPL.KPKI.KKRTKKFI.HQSDRYVKIK...........RV.RR.KGQI.MPSIGYGSNKKTKHML
Retrocopy MATLRPLMKPKIAKKRTKKFIWHQSDRYVKIKRNWWKPRGIDSRVCRRFKGQILMPSIGYGSNKKTKHML

Parental  PSGFRKFLVHNVMEHEV-VMCN
          PSGFRKFLVHNV.E.EV..MCN
Retrocopy PSGFRKFLVHNVKELEVLLMCN

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_17 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_17 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 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Vicugna pacos	ENSVPAG00000002594	1 retrocopy	retro_vpac_17 ,