RetrogeneDB ID: retro_vpac_340

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_10346:11028..11689(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSVPAG00000003701
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_vpac_340
TCCGTGGTCCCGCCCAGTAGCTCGCAGACTGCTGGCCCCGGGGTCAACCAGTTCGGCAACAAGTACGTCCAGCAGACCAA
GCCCCTCACCCTGGAGCGTGCTATGAACCTGTAACCTCTTACCGATTAAACTTTTGGTATAAAAGAGCCCCTCTATGAGA
AGGGCAGCTCTGTTGCGGCCAGATGTCAGCGTTTGAGGGAGGGATTTGATAAAATTGGCATGAGAATGATTGTAGAAGGG
GTTCTGATTGTCCATGAGCACCGTCTGCCCGACGTGTTAACTGCCACAGCTGCCAACAGCTTTCTTCAAATTACCTGGTG
GTGAGCTTAACCCCAGAGAAGATGAAGTGGAAGGACTAAAATGCTTAATGACAGAGATACTGGATCGTCAAGATGGAGTC
CTGCAAGACTGGGTCACTGACTACTGCATTGGTAACTGGTGGAGAACAAATTTTGAACCTCCTCAGTGTCCATATATTCC
TGCACACATTGCAAAACCTAAGGAACATAAGAAGTTGTGTTTGGTTCAACTTCAAGAGAAAGCCTTGTTTGCAATTCCTA
AAAATTACAAGCTGGTAGCTGCACCGCTGTTTGAACTGTATGACAATGCGCCTGGATATGGACCCATTTCTAGTCTCCCT
CAGCTTTTGTGCATATACAAC

Alignment

ORF - retro_vpac_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 97.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVVPPNRSQTGWPRGVNQFGNKYIQQTKPLTLERTINLYPLTNYTFGTKEPLYEKDSSVAARFQRMREEF
          SVVPP..SQT..P.GVNQFGNKY.QQTKPLTLER..NL.PLT..TFG.KEPLYEK.SSVAAR.QR.RE.F
Retrocopy SVVPPSSSQTAGP-GVNQFGNKYVQQTKPLTLERAMNL*PLTD*TFGIKEPLYEKGSSVAARCQRLREGF

Parental  DKIGMRRTVEGVLIVHEHRLPHVL-LLQLGTTFFKLPGGELNPGEDEVEGLKRLMTELLGRQDGVLQDWV
          DKIGMR..VEGVLIVHEHRLP.VL.L.QL.T.FFKLPGGELNP.EDEVEGLK.LMTE.L.RQDGVLQDWV
Retrocopy DKIGMRMIVEGVLIVHEHRLPDVL>LPQLPTAFFKLPGGELNPREDEVEGLKCLMTEILDRQDGVLQDWV

Parental  IDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQLQEKALFAVPKNYKLVAAPLFELYDNAPGYGP
          .D.CIGNWWR.NFEPPQ.PYIPAHI.KPKEHKKL.LVQLQEKALFA.PKNYKLVAAPLFELYDNAPGYGP
Retrocopy TDYCIGNWWRTNFEPPQCPYIPAHIAKPKEHKKLCLVQLQEKALFAIPKNYKLVAAPLFELYDNAPGYGP

Parental  IISSLPQLLSRFN
          I.SSLPQLL...N
Retrocopy I-SSLPQLLCIYN

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_340 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_340 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016628	1 retrocopy	retro_amel_540,
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Equus caballus	ENSECAG00000001043	1 retrocopy	retro_ecab_292,
Erinaceus europaeus	ENSEEUG00000003402	1 retrocopy	retro_eeur_35,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Myotis lucifugus	ENSMLUG00000004968	2 retrocopies	retro_mluc_1576, retro_mluc_999,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tupaia belangeri	ENSTBEG00000007664	1 retrocopy	retro_tbel_4003,
Vicugna pacos	ENSVPAG00000003701	2 retrocopies	retro_vpac_340 , retro_vpac_605,