RetrogeneDB ID: retro_vpac_226

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: GeneScaffold_3018:114349..114960(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NQO1
• Ensembl ID: ENSVPAG00000002038
• Aliases: None
• Description: NAD(P)H dehydrogenase, quinone 1 [Source:HGNC Symbol;Acc:2874]

Sequence

>retro_vpac_226
ACCGTTCTAACTTATAAAGAAGGCAGCCTGAGCCCAGATATTGTGATTGAACAAAAGAAGCTGGAAGCGGCAGACCTGGT
CATTTTTCAGTTCCCACTGCAGTGATTTGGGGTCCCTGCTATCCTGAAAGGCTGGTTTGAACGCATGCTCATAGGGAAGT
TTGCTTACATGTATGCTGCCATGTATGACAAGGGACCTTTCTGGAATAAGAAGGCAGTCTTTCCATCACCACTGGTGGCA
GCGGCTCCATGTACTCTCTGCAGGGTATCCACGGGGACTTGAATATTATTCTCTGGCCCATTCAGAGTGGCGCTCTGCAT
TTCTGTGGCTTCCAAGTCTTGGAACCTCAACTGACATAATAGCATTGGCCACACTCCCGAGGATGCCAGAATTCAGATCC
CGGAAGGATGGAAGAAACGCCTGGAGAATATTTGGGATGAGACGCCGCTGTGTTTTGCTCCAAGTAGCCTCTTTGACCTA
AATTTCCAGGCAGGATATTCTTAGTGAAAAAGGAGATGCAGGATGAGCAAAAAAATAAGAAATTAGGCTTTTCTGTGGGC
CATCACTTGGGCAAGCCCATCCCAGTGGACAACCAGATCAAAGCTGGAAAA

Alignment

ORF - retro_vpac_226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 74.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVLAYKEGRLSPDIVAEQKKLEAADLVIFQFPLQWFGVPAILKGWFERVLIGEFAYTYAAMYDKGPFRNK
          .VL.YKEG.LSPDIV.EQKKLEAADLVIFQFPLQ.FGVPAILKGWFER.LIG.FAY.YAAMYDKGPF.NK
Retrocopy TVLTYKEGSLSPDIVIEQKKLEAADLVIFQFPLQ*FGVPAILKGWFERMLIGKFAYMYAAMYDKGPFWNK

Parental  KAV-LSITTGGSGSMYSLQGIHGDMNIILWPIQSGTLHFCGFQVLEPQLT-YSIGHTPEDARIQILEGWK
          KAV.LSITTGGSGSMYSLQGIHGD.NIILWPIQSG.LHFCGFQVLEPQLT..SIGHTPEDARIQI.EGWK
Retrocopy KAV<LSITTGGSGSMYSLQGIHGDLNIILWPIQSGALHFCGFQVLEPQLT>NSIGHTPEDARIQIPEGWK

Parental  KRLENIWDETPLYFAPSSLFDLNFQAGF-LMKKEVQDEQ-KNKNFGLSVGHHLGKPIPADNQIKARK
          KRLENIWDETPL.FAPSSLFDLNFQAG.....K.......KNK..G.SVGHHLGKPIP.DNQIKA.K
Retrocopy KRLENIWDETPLCFAPSSLFDLNFQAGY<FLVKKEMQDEQKNKKLGFSVGHHLGKPIPVDNQIKAGK

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_226 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_226 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000004589	1 retrocopy	retro_ogar_2667,
Vicugna pacos	ENSVPAG00000002038	1 retrocopy	retro_vpac_226 ,