RetrogeneDB ID: retro_vpac_372

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_13232:6963..7466(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSN1
• Ensembl ID: ENSVPAG00000003601
• Aliases: None
• Description: DSN1, MIS12 kinetochore complex component [Source:HGNC Symbol;Acc:16165]

Sequence

>retro_vpac_372
AGTCTTGAAAGTTTTAGAAGCAAAGCATTTTCTCTTTCTGAAGAATTTAAATATTTGCAGTCAGTGGAAAATGATGGAAG
CCTACGAAAATGTTCTGACAATCCAAAGGAAAAGCATCGTATTTGTCTCCAGAAACATCAGTGGCTGAGATGAAGGAATG
CACAGCCAAGCTTTCTTTAGAATGCCAAAGCTGAGGTCAGGACTTGCTGCACCATCACAATGGATGTGACTTATTACATG
ATACAGGGATCAACCAAAGCCAAAATGACTCATATTGAAGTGGAACCAGTGATGTATCTTGATCTTTCCAGTGCAAAGTT
CTTCACTCAAATCCTGACCACCGGAAGGTATTACAGAACCAGCGCAAGGTCTCTGATGGTACGCAGTTTGTGATAGATGG
ACCGCAGTGATCAGTGGGGCACCTGCAGGTCTTTACGGGCAAAAGTACTCAGTGTTTCCAGAAGGGGTCAGTACAGCTTG
GGAAGAGAAGCAGCAAACAGATC

Alignment

ORF - retro_vpac_372 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.58 %
• Parental protein coverage: 71.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NLESYKAKASSLSEELKHFADSLEGNGALQKCFEDPE-GRASDLSLETSVAEMKEYITKFSLERQSWDQL
          .LES...KA.SLSEE.K....S.E..G.L.KC...P..G.AS.LS.ETSVAEMKE...K.SLE.QS..Q.
Retrocopy SLESFRSKAFSLSEEFKYL-QSVENDGSLRKCSDNPK<GKASYLSPETSVAEMKECTAKLSLECQS*GQD

Parental  LLRYQEEAEKI-ISRGSTETKNTEVEVGPTTYLR-SSQSEVLNTKPDYQKILQNQNKVFDCMELVMDELQ
          LL.............GST..K.T..EV.P..YL..S.Q..VL...PD..K.LQNQ.KV.D....V.D..Q
Retrocopy LLHHHNGCDLL>MIQGSTKAKMTHIEVEPVMYLD<SFQCKVLHSNPDHRKVLQNQRKVSDGTQFVIDGPQ

Parental  GSVKQLHTFMDESTQCLQKVSVQLGKRSTQQL
          .SV..L..F...STQC.QK.SVQLGKRS..Q.
Retrocopy *SVGHLQVFTGKSTQCFQKGSVQLGKRSSKQI

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_372 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_372 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
Tupaia belangeri	ENSTBEG00000002396	1 retrocopy	retro_tbel_2103,
Vicugna pacos	ENSVPAG00000003601	1 retrocopy	retro_vpac_372 ,